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  • 101
    Publikationsdatum: 2021-08-03
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 102
    Publikationsdatum: 2021-03-05
    Beschreibung: Understanding the pathophysiological processes of cartilage degradation requires adequate model systems to develop therapeutic strategies towards osteoarthritis (OA). Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific disease aspects. This study aimed to combine in vitro and in silico modeling based on a tissue-engineering approach using mesenchymal condensation to mimic cytokine-induced cellular and matrix-related changes during cartilage degradation. Thus, scaffold-free cartilage-like constructs (SFCCs) were produced based on self-organization of mesenchymal stromal cells (mesenchymal condensation) and i) characterized regarding their cellular and matrix composition or secondly ii) treated with interleukin-1β (IL-1β) and tumor necrosis factor α (TNFα) for 3 weeks to simulate OA-related matrix degradation. In addition, an existing mathematical model based on partial differential equations was optimized and transferred to the underlying settings to simulate distribution of IL-1β, type II collagen degradation and cell number reduction. By combining in vitro and in silico methods, we aim to develop a valid, efficient alternative approach to examine and predict disease progression and effects of new therapeutics.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 103
    Publikationsdatum: 2021-10-28
    Beschreibung: Motivated by the desire to numerically calculate rigorous upper and lower bounds on deviation probabilities over large classes of probability distributions, we present an adaptive algorithm for the reconstruction of increasing real-valued functions. While this problem is similar to the classical statistical problem of isotonic regression, the optimisation setting alters several characteristics of the problem and opens natural algorithmic possibilities. We present our algorithm, establish sufficient conditions for convergence of the reconstruction to the ground truth, and apply the method to synthetic test cases and a real-world example of uncertainty quantification for aerodynamic design.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 104
    Publikationsdatum: 2020-09-14
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 105
    Publikationsdatum: 2021-04-16
    Sprache: Englisch
    Materialart: reportzib , doc-type:preprint
    Format: application/pdf
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  • 106
    Publikationsdatum: 2021-02-23
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 107
    Publikationsdatum: 2021-03-26
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 108
    Publikationsdatum: 2021-02-23
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 109
    Publikationsdatum: 2022-03-14
    Beschreibung: It is a challenging task to fairly compare local solvers and heuristics against each other and against global solvers. How does one weigh a faster termination time against a better quality of the found solution? In this paper, we introduce the confined primal integral, a new performance measure that rewards a balance of speed and solution quality. It emphasizes the early part of the solution process by using an exponential decay. Thereby, it avoids that the order of solvers can be inverted by choosing an arbitrarily large time limit. We provide a closed analytic formula to compute the confined primal integral a posteriori and an incremental update formula to compute it during the run of an algorithm. For the latter, we show that we can drop one of the main assumptions of the primal integral, namely the knowledge of a fixed reference solution to compare against. Furthermore, we prove that the confined primal integral is a transitive measure when comparing local solves with different final solution values. Finally, we present a computational experiment where we compare a local MINLP solver that uses certain classes of cutting planes against a solver that does not. Both versions show very different tendencies w.r.t. average running time and solution quality, and we use the confined primal integral to argue which of the two is the preferred setting.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 110
    Publikationsdatum: 2021-02-22
    Sprache: Englisch
    Materialart: bookpart , doc-type:bookPart
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  • 111
    Publikationsdatum: 2022-03-14
    Beschreibung: The Periodic Event Scheduling Problem is a well-studied NP-hard problem with applications in public transportation to find good periodic timetables. Among the most powerful heuristics to solve the periodic timetabling problem is the modulo network simplex method. In this paper, we consider the more difficult version with integrated passenger routing and propose a refined integrated variant to solve this problem on real-world-based instances.
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 112
    Publikationsdatum: 2021-02-05
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 113
    Publikationsdatum: 2022-03-14
    Beschreibung: Dual degeneracy, i.e., the presence of multiple optimal bases to a linear programming (LP) problem, heavily affects the solution process of mixed integer programming (MIP) solvers. Different optimal bases lead to different cuts being generated, different branching decisions being taken and different solutions being found by primal heuristics. Nevertheless, only a few methods have been published that either avoid or exploit dual degeneracy. The aim of the present paper is to conduct a thorough computational study on the presence of dual degeneracy for the instances of well-known public MIP instance collections. How many instances are affected by dual degeneracy? How degenerate are the affected models? How does branching affect degeneracy: Does it increase or decrease by fixing variables? Can we identify different types of degenerate MIPs? As a tool to answer these questions, we introduce a new measure for dual degeneracy: the variable–constraint ratio of the optimal face. It provides an estimate for the likelihood that a basic variable can be pivoted out of the basis. Furthermore, we study how the so-called cloud intervals—the projections of the optimal face of the LP relaxations onto the individual variables—evolve during tree search and the implications for reducing the set of branching candidates.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 114
    Publikationsdatum: 2021-04-20
    Beschreibung: This article is mainly motivated by the urge to answer two kinds of questions regarding the Bundesliga, which is Germany’s primary football (soccer) division having the highest average stadium attendance worldwide: “At any point in the season, what is the lowest final rank a certain team can achieve?” and “At any point in the season, what is the highest final rank a certain team can achieve?”. Although we focus on the Bundesliga in particular, the integer programming formulations we introduce to answer these questions can easily be adapted to a variety of other league systems and tournaments.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 115
    Publikationsdatum: 2021-07-06
    Beschreibung: Markov chain (MC) algorithms are ubiquitous in machine learning and statistics and many other disciplines. Typically, these algorithms can be formulated as acceptance rejection methods. In this work we present a novel estimator applicable to these methods, dubbed Markov chain importance sampling (MCIS), which efficiently makes use of rejected proposals. For the unadjusted Langevin algorithm, it provides a novel way of correcting the discretization error. Our estimator satisfies a central limit theorem and improves on error per CPU cycle, often to a large extent. As a by-product it enables estimating the normalizing constant, an important quantity in Bayesian machine learning and statistics.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 116
    Publikationsdatum: 2021-02-23
    Beschreibung: The presence of a confining boundary can modify the local structure of a liquid markedly. In addition, small samples of finite size are known to exhibit systematic deviations of thermodynamic quantities relative to their bulk values. Here, we consider the static structure factor of a liquid sample in slab geometry with open boundaries at the surfaces, which can be thought of as virtually cutting out the sample from a macroscopically large, homogeneous fluid. This situation is a relevant limit for the interpretation of grazing-incidence diffraction experiments at liquid interfaces and films. We derive an exact, closed expression for the slab structure factor, with the bulk structure factor as the only input. This shows that such free boundary conditions cause significant differences between the two structure factors, in particular, at small wavenumbers. An asymptotic analysis of this result yields the scaling exponent and an accurate, useful approximation of these finite-size corrections. Furthermore, the open boundaries permit the interpretation of the slab as an open system, supporting particle exchange with a reservoir. We relate the slab structure factor to the particle number fluctuations and discuss conditions under which the subvolume of the slab represents a grand canonical ensemble with chemical potential μ and temperature T. Thus, the open slab serves as a test-bed for the small-system thermodynamics in a μT reservoir. We provide a microscopically justified and exact result for the size dependence of the isothermal compressibility. Our findings are corroborated by simulation data for Lennard-Jones liquids at two representative temperatures.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 117
    Publikationsdatum: 2021-10-26
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 118
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 119
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 120
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 121
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: masterthesis , doc-type:masterThesis
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  • 122
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 123
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 124
  • 125
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: researchdata , doc-type:ResearchData
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  • 126
    Publikationsdatum: 2022-06-13
    Beschreibung: Large capacity Storage Class Memory (SCM) opens new possibilities for workloads requiring a large memory footprint. We examine optimization strategies for a legacy Fortran application on systems with an heterogeneous memory configuration comprising SCM and DRAM. We present a performance study for the multigrid solver component of the large-eddy simulation framework PALM for different memory configurations with large capacity SCM. An important optimization approach is the explicit assignment of storage locations depending on the data access characteristic to take advantage of the heterogeneous memory configuration. We are able to demonstrate that an explicit control over memory locations provides better performance compared to transparent hardware settings. As on aforementioned systems the page management by the OS appears as critical performance factor, we study the impact of different huge page settings.
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 127
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 128
    Publikationsdatum: 2022-06-13
    Sprache: Englisch
    Materialart: other , doc-type:Other
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  • 129
    Publikationsdatum: 2022-06-27
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 130
    Publikationsdatum: 2022-06-27
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 131
    Publikationsdatum: 2022-06-27
    Beschreibung: In this article we introduce a Minimum Cycle Partition Problem with Length Requirements (CPLR). This generalization of the Travelling Salesman Problem (TSP) originates from routing Unmanned Aerial Vehicles (UAVs). Apart from nonnegative edge weights, CPLR has an individual critical weight value associated with each vertex. A cycle partition, i.e., a vertex disjoint cycle cover, is regarded as a feasible solution if the length of each cycle, which is the sum of the weights of its edges, is not greater than the critical weight of each of its vertices. The goal is to find a feasible partition, which minimizes the number of cycles. In this article, a heuristic algorithm is presented together with a Mixed Integer Programming (MIP) formulation of CPLR. We furthermore introduce a conflict graph, whose cliques yield valid constraints for the MIP model. Finally, we report on computational experiments conducted on TSPLIB-based test instances.
    Sprache: Englisch
    Materialart: bookpart , doc-type:bookPart
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  • 132
    Publikationsdatum: 2022-07-07
    Sprache: Englisch
    Materialart: bookpart , doc-type:bookPart
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  • 133
    Publikationsdatum: 2022-07-19
    Beschreibung: Surgical tool segmentation in endoscopic videos is an important component of computer assisted interventions systems. Recent success of image-based solutions using fully-supervised deep learning approaches can be attributed to the collection of big labeled datasets. However, the annotation of a big dataset of real videos can be prohibitively expensive and time consuming. Computer simulations could alleviate the manual labeling problem, however, models trained on simulated data do not generalize to real data. This work proposes a consistency-based framework for joint learning of simulated and real (unlabeled) endoscopic data to bridge this performance generalization issue. Empirical results on two data sets (15 videos of the Cholec80 and EndoVis'15 dataset) highlight the effectiveness of the proposed Endo-Sim2Real method for instrument segmentation. We compare the segmentation of the proposed approach with state-of-the-art solutions and show that our method improves segmentation both in terms of quality and quantity.
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 134
    Publikationsdatum: 2022-07-19
    Beschreibung: An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 135
    Publikationsdatum: 2022-07-19
    Beschreibung: Automatic recognition of surgical phases is an important component for developing an intra-operative context-aware system. Prior work in this area focuses on recognizing short-term tool usage patterns within surgical phases. However, the difference between intra- and inter-phase tool usage patterns has not been investigated for automatic phase recognition. We developed a Recurrent Neural Network (RNN), in particular a state-preserving Long Short Term Memory (LSTM) architecture to utilize the long-term evolution of tool usage within complete surgical procedures. For fully automatic tool presence detection from surgical video frames, a Convolutional Neural Network (CNN) based architecture namely ZIBNet is employed. Our proposed approach outperformed EndoNet by 8.1% on overall precision for phase detection tasks and 12.5% on meanAP for tool recognition tasks.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 136
    Publikationsdatum: 2022-07-19
    Beschreibung: We propose generalizations of the T²-statistics of Hotelling and the Bhattacharayya distance for data taking values in Lie groups. A key feature of the derived measures is that they are compatible with the group structure even for manifolds that do not admit any bi-invariant metric. This property, e.g., assures analysis that does not depend on the reference shape, thus, preventing bias due to arbitrary choices thereof. Furthermore, the generalizations agree with the common definitions for the special case of flat vector spaces guaranteeing consistency. Employing a permutation test setup, we further obtain nonparametric, two-sample testing procedures that themselves are bi-invariant and consistent. We validate our method in group tests revealing significant differences in hippocampal shape between individuals with mild cognitive impairment and normal controls.
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 137
    Publikationsdatum: 2022-07-19
    Beschreibung: Motivation: The ever-rising volume of patients, high maintenance cost of operating rooms and time consuming analysis of surgical skills are fundamental problems that hamper the practical training of the next generation of surgeons. The hospitals prefer to keep the surgeons busy in real operations over training young surgeons for obvious economic reasons. One fundamental need in surgical training is the reduction of the time needed by the senior surgeon to review the endoscopic procedures performed by the young surgeon while minimizing the subjective bias in evaluation. The unprecedented performance of deep learning ushers the new age of data-driven automatic analysis of surgical skills. Method: Deep learning is capable of efficiently analyzing thousands of hours of laparoscopic video footage to provide an objective assessment of surgical skills. However, the traditional end-to-end setting of deep learning (video in, skill assessment out) is not explainable. Our strategy is to utilize the surgical process modeling framework to divide the surgical process into understandable components. This provides the opportunity to employ deep learning for superior yet automatic detection and evaluation of several aspects of laparoscopic cholecystectomy such as surgical tool and phase detection. We employ ZIBNet for the detection of surgical tool presence. ZIBNet employs pre-processing based on tool usage imbalance, a transfer learned 50-layer residual network (ResNet-50) and temporal smoothing. To encode the temporal evolution of tool usage (over the entire video sequence) that relates to the surgical phases, Long Short Term Memory (LSTM) units are employed with long-term dependency. Dataset: We used CHOLEC 80 dataset that consists of 80 videos of laparoscopic cholecystectomy performed by 13 surgeons, divided equally for training and testing. In these videos, up to three different tools (among 7 types of tools) can be present in a frame. Results: The mean average precision of the detection of all tools is 93.5 ranging between 86.8 and 99.3, a significant improvement (p 〈0.01) over the previous state-of-the-art. We observed that less frequent tools like Scissors, Irrigator, Specimen Bag etc. are more related to phase transitions. The overall precision (recall) of the detection of all surgical phases is 79.6 (81.3). Conclusion: While this is not the end goal for surgical skill analysis, the development of such a technological platform is essential toward a data-driven objective understanding of surgical skills. In future, we plan to investigate surgeon-in-the-loop analysis and feedback for surgical skill analysis.
    Sprache: Englisch
    Materialart: other , doc-type:Other
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  • 138
    Publikationsdatum: 2022-07-19
    Beschreibung: The images of D’Arcy Wentworth Thompson’s book “On Growth and Form” got an iconic status and became influential for biometrics and other mathematical approaches to organismic form. In particular, this is true for those of the chapter on the theory of transformation, which even has an impact on art and humanities. Based on his approach, Thompson formulated far-reaching conclusions with a partly anti-Darwinian stance. Here, we use the example of Thompson’s transformation of crab carapaces to test to what degree the transformation of grids, landmarks, and shapes result in congruent images. For comparison, we applied the same series of tests to digitized carapaces of real crabs. Both approaches show similar results. Only the simple transformations show a reasonable form of congruence. In particular, the transformations to majoid spider crabs reveal a complicated transformation of grids with partly crossing lines. By contrast, the carapace of the lithodid species is relatively easily created despite the fact that it is no brachyuran, but evolved a spider crab-like shape convergently from a hermit crab ancestor.
    Sprache: Englisch
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  • 139
    Publikationsdatum: 2022-07-19
    Beschreibung: Intrinsic and parametric regression models are of high interest for the statistical analysis of manifold-valued data such as images and shapes. The standard linear ansatz has been generalized to geodesic regression on manifolds making it possible to analyze dependencies of random variables that spread along generalized straight lines. Nevertheless, in some scenarios, the evolution of the data cannot be modeled adequately by a geodesic. We present a framework for nonlinear regression on manifolds by considering Riemannian splines, whose segments are Bézier curves, as trajectories. Unlike variational formulations that require time-discretization, we take a constructive approach that provides efficient and exact evaluation by virtue of the generalized de Casteljau algorithm. We validate our method in experiments on the reconstruction of periodic motion of the mitral valve as well as the analysis of femoral shape changes during the course of osteoarthritis, endorsing Bézier spline regression as an effective and flexible tool for manifold-valued regression.
    Sprache: Englisch
    Materialart: conferenceobject , doc-type:conferenceObject
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  • 140
    Publikationsdatum: 2022-07-19
    Beschreibung: A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach.
    Sprache: Englisch
    Materialart: reportzib , doc-type:preprint
    Format: application/pdf
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  • 141
    Publikationsdatum: 2022-07-19
    Beschreibung: In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 142
    Publikationsdatum: 2022-07-19
    Beschreibung: This study’s objective was the generation of a standardized geometry of the healthy nasal cavity. An average geometry of the healthy nasal cavity was generated using a statistical shape model based on 25 symptom-free subjects. Airflow within the average geometry and these geometries was calculated using fluid simulations. Integral measures of the nasal resistance, wall shear stresses (WSS) and velocities were calculated as well as cross-sectional areas (CSA). Furthermore, individual WSS and static pressure distributions were mapped onto the average geometry. The average geometry featured an overall more regular shape that resulted in less resistance, reduced wall shear stresses and velocities compared to the median of the 25 geometries. Spatial distributions of WSS and pressure of average geometry agreed well compared to the average distributions of all individual geometries. The minimal CSA of the average geometry was larger than the median of all individual geometries (83.4 vs. 74.7 mm²). The airflow observed within the average geometry of the healthy nasal cavity did not equal the average airflow of the individual geometries. While differences observed for integral measures were notable, the calculated values for the average geometry lay within the distributions of the individual parameters. Spatially resolved parameters differed less prominently.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 143
    Publikationsdatum: 2022-07-19
    Beschreibung: We present time-space trade-offs for computing the Euclidean minimum spanning tree of a set S of n point-sites in the plane. More precisely, we assume that S resides in a random-access memory that can only be read. The edges of the Euclidean minimum spanning tree EMST(S) have to be reported sequentially, and they cannot be accessed or modified afterwards. There is a parameter s in {1, ..., n} so that the algorithm may use O(s) cells of read-write memory (called the workspace) for its computations. Our goal is to find an algorithm that has the best possible running time for any given s between 1 and n. We show how to compute EMST(S) in O(((n^3)/(s^2)) log s) time with O(s) cells of workspace, giving a smooth trade-off between the two best-known bounds O(n^3) for s = 1 and O(n log n) for s = n. For this, we run Kruskal's algorithm on the "relative neighborhood graph" (RNG) of S. It is a classic fact that the minimum spanning tree of RNG(S) is exactly EMST(S). To implement Kruskal's algorithm with O(s) cells of workspace, we define s-nets, a compact representation of planar graphs. This allows us to efficiently maintain and update the components of the current minimum spanning forest as the edges are being inserted.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 144
    Publikationsdatum: 2022-07-19
    Beschreibung: In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone.
    Sprache: Englisch
    Materialart: reportzib , doc-type:preprint
    Format: application/pdf
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  • 145
    Publikationsdatum: 2022-07-19
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 146
    Publikationsdatum: 2022-07-19
    Beschreibung: An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time.
    Sprache: Englisch
    Materialart: reportzib , doc-type:preprint
    Format: application/pdf
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  • 147
    Publikationsdatum: 2022-07-19
    Beschreibung: We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 148
    Publikationsdatum: 2022-07-19
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 149
    Publikationsdatum: 2022-07-19
    Beschreibung: Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 150
    Publikationsdatum: 2022-07-19
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 151
    Publikationsdatum: 2022-07-19
    Beschreibung: We analytically determine Jacobi fields and parallel transports and compute geodesic regression in Kendall’s shape space. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and thereby reduce the computational expense by several orders of magnitude over common, nonlinear constrained approaches. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As an example application we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative (OAI). Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data alone.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 152
    Publikationsdatum: 2022-07-19
    Beschreibung: A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 153
    Publikationsdatum: 2022-07-19
    Beschreibung: Conflicting hypotheses about the relationships among the major lineages of aculeate Hymenoptera clearly show the necessity of detailed comparative morphological studies. Using micro-computed tomography and 3D reconstructions, the skeletal musculature of the meso- and metathorax and the first and second abdominal segment in Apoidea are described. Females of Sceliphron destillatorium, Sphex (Fernaldina) lucae (both Sphecidae), and Ampulex compressa (Ampulicidae) were examined. The morphological terminology provided by the Hymenoptera Anatomy Ontology is used. Up to 42 muscles were found. The three species differ in certain numerical and structural aspects. Ampulicidae differs significantly from Sphecidae in the metathorax and the anterior abdomen. The metapleural apodeme and paracoxal ridge are weakly developed in Ampulicidae, which affect some muscular structures. Furthermore, the muscles that insert on the coxae and trochanters are broader and longer in Ampulicidae. A conspicuous characteristic of Sphecidae is the absence of the metaphragma. Overall, we identified four hitherto unrecognized muscles. Our work suggests additional investigations on structures discussed in this paper.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 154
    Publikationsdatum: 2022-07-19
    Beschreibung: We present an automated method for extrapolating missing regions in label data of the skull in an anatomically plausible manner. The ultimate goal is to design patient-speci� c cranial implants for correcting large, arbitrarily shaped defects of the skull that can, for example, result from trauma of the head. Our approach utilizes a 3D statistical shape model (SSM) of the skull and a 2D generative adversarial network (GAN) that is trained in an unsupervised fashion from samples of healthy patients alone. By � tting the SSM to given input labels containing the skull defect, a First approximation of the healthy state of the patient is obtained. The GAN is then applied to further correct and smooth the output of the SSM in an anatomically plausible manner. Finally, the defect region is extracted using morphological operations and subtraction between the extrapolated healthy state of the patient and the defective input labels. The method is trained and evaluated based on data from the MICCAI 2020 AutoImplant challenge. It produces state-of-the art results on regularly shaped cut-outs that were present in the training and testing data of the challenge. Furthermore, due to unsupervised nature of the approach, the method generalizes well to previously unseen defects of varying shapes that were only present in the hidden test dataset.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 155
    Publikationsdatum: 2022-09-22
    Beschreibung: A new virtual unfolding technique was applied to a silver scroll excavated in Jerash, Jordan, in 2014. As result of the unfolding, 17 lines of writing are clearly visible in the unfolded volumetric data that is published here.
    Sprache: Englisch
    Materialart: researchdata , doc-type:ResearchData
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  • 156
    Publikationsdatum: 2022-11-28
    Sprache: Englisch
    Materialart: book , doc-type:book
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  • 157
  • 158
    Publikationsdatum: 2022-11-28
    Sprache: Englisch
    Materialart: incollection , doc-type:Other
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  • 159
    Publikationsdatum: 2022-11-28
    Beschreibung: We present a novel kernel-based machine learning algorithm for identifying the low-dimensional geometry of the effective dynamics of high-dimensional multiscale stochastic systems. Recently, the authors developed a mathematical framework for the computation of optimal reaction coordinates of such systems that is based on learning a parameterization of a low-dimensional transition manifold in a certain function space. In this article, we enhance this approach by embedding and learning this transition manifold in a reproducing kernel Hilbert space, exploiting the favorable properties of kernel embeddings. Under mild assumptions on the kernel, the manifold structure is shown to be preserved under the embedding, and distortion bounds can be derived. This leads to a more robust and more efficient algorithm compared to the previous parameterization approaches.
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 160
    facet.materialart.
    Unbekannt
    Publikationsdatum: 2022-11-28
    Beschreibung: Markov State Models (MSM) sind der Goldstandard zur Modellierung biomolekularer Dynamik, da sie die Identifizierung und Analyse metastabiler Zustände ermöglichen. Die robuste Perron-Cluster-Cluster-Analyse (PCCA+) ist ein verbreiteter Spectral-Clustering-Algorithmus, der für das Clustering hochdimensionaler MSM verwendet wird. Da die PCCA+ auf reversible Prozesse beschränkt ist, wird sie zur Generalisierten PCCA+ (G-PCCA) verallgemeinert, die geeignet ist, nichtreversible Prozesse aufzuklären. Bernhard Reuter untersucht hier mittels G-PCCA die nichtthermischen Auswirkungen von Mikrowellen auf die Proteindynamik. Dazu führt er molekulardynamische Nichtgleichgewichtssimulationen des Amyloid-β-(1–40)-Peptids durch und modelliert diese.
    Sprache: Deutsch
    Materialart: book , doc-type:book
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  • 161
    Publikationsdatum: 2022-11-28
    Sprache: Englisch
    Materialart: incollection , doc-type:Other
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  • 162
    Publikationsdatum: 2022-11-28
    Beschreibung: Model reduction of large Markov chains is an essential step in a wide array of techniques for understanding complex systems and for efficiently learning structures from high-dimensional data. We present a novel aggregation algorithm for compressing such chains that exploits a specific low-rank structure in the transition matrix which, e.g., is present in metastable systems, among others. It enables the recovery of the aggregates from a vastly undersampled transition matrix which in practical applications may gain a speedup of several orders of mag- nitude over methods that require the full transition matrix. Moreover, we show that the new technique is robust under perturbation of the transition matrix. The practical applicability of the new method is demonstrated by identifying a reduced model for the large-scale traffic flow patterns from real-world taxi trip data.
    Sprache: Englisch
    Materialart: reportzib , doc-type:preprint
    Format: application/pdf
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  • 163
    Publikationsdatum: 2022-12-05
    Sprache: Englisch
    Materialart: article , doc-type:article
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  • 164
    Buch
    Buch
    Wien [u.a.] :Springer, ; 1.1977 - 16.2003; damit Ersch. eingest.
    Titel: Computing : archives for informatics and numerical computation; Supplementum
    Verlag: Wien [u.a.] :Springer,
    Erscheinungsjahr: 1977-2003
    Erscheinungsverlauf: 1.1977 - 16.2003; damit Ersch. eingest.
    Materialart: Buch
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 165
    Online-Ressource
    Online-Ressource
    Berlin ; Heidelberg :Springer, ; 1.1995(1996) - 8.2002
    Titel: Journal of molecular modeling
    Verlag: Berlin ; Heidelberg :Springer,
    Erscheinungsjahr: 1996-2002
    Erscheinungsverlauf: 1.1995(1996) - 8.2002
    ISSN: 0949-183X
    Materialart: Online-Ressource
    Sprache: Unbestimmte Sprache
    Nachfolgender Titel: Forts. ---〉:Journal of molecular modeling
    Anmerkung: Kumuliert jeweils den abgeschlossenen Jg. der Internetausg.
    Paralleltitel: Druckausg. ---〉:Molecular modeling annual
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  • 166
    Zeitschrift/Serie
    Zeitschrift/Serie
    New York, NY :ACM, ; 1.1969 - 7.1975/76; N.S. 1.1976 - 21.2001,1; damit Ersch. eingest.
    Titel: SIGBIO newsletter /
    Autor: Association for Computing Machinery / Special Interest Group on Biomedical Computing
    Verlag: New York, NY :ACM,
    Erscheinungsjahr: 1969-2001
    Erscheinungsverlauf: 1.1969 - 7.1975/76; N.S. 1.1976 - 21.2001,1; damit Ersch. eingest.
    ISSN: 0163-5697
    Materialart: Zeitschrift/Serie
    Sprache: Unbestimmte Sprache
    Paralleltitel: Internetausg. ---〉:Biomedical computing
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 167
    Zeitschrift/Serie
    Zeitschrift/Serie
    Los Alamitos, Calif. :Soc., ; 5.1997 - 8.2000; damit Ersch. eingest.
    Titel: IEEE concurrency /
    Autor: Institute of Electrical and Electronics Engineers / Computer Group
    Verlag: Los Alamitos, Calif. :Soc.,
    Erscheinungsjahr: 1997-2000
    Erscheinungsverlauf: 5.1997 - 8.2000; damit Ersch. eingest.
    ISSN: 1092-3063
    Materialart: Zeitschrift/Serie
    Sprache: Unbestimmte Sprache
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 168
    Zeitschrift/Serie
    Zeitschrift/Serie
    New York, NY :North-Holland, ; 1.1984 - 46.2000
    Titel: ¬The¬ journal of logic programming
    Verlag: New York, NY :North-Holland,
    Erscheinungsjahr: 1984-2000
    Erscheinungsverlauf: 1.1984 - 46.2000
    ISSN: 0743-1066
    Materialart: Zeitschrift/Serie
    Sprache: Unbestimmte Sprache
    Nachfolgender Titel: Forts. ---〉:¬The¬ journal of logic and algebraic programming
    Paralleltitel: Internetausg. ---〉:¬The¬ journal of logic and algebraic programming
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  • 169
    Zeitschrift/Serie
    Zeitschrift/Serie
    Amsterdam :CWI, ; 1.1988 - 12.1999; damit Ersch. eingest.
    Titel: CWI quarterly
    Autor: Centrum voor Wiskunde en Informatica 〈Amsterdam〉
    Verlag: Amsterdam :CWI,
    Erscheinungsjahr: 1988-1999
    Erscheinungsverlauf: 1.1988 - 12.1999; damit Ersch. eingest.
    ISSN: 0168-826X , 0922-5366
    Materialart: Zeitschrift/Serie
    Sprache: Unbestimmte Sprache
    Vorheriger Titel: Vorg. ---〉:Centrum voor Wiskunde en Informatica 〈Amsterdam〉: CWI newsletter
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  • 170
    E-Ressource
    E-Ressource
    Oxford :Univ. Press, ; 1.1996/97 - 3.1999; damit Ersch. eingest.
    Titel: Medical image analysis CD : an international journal of computer vision, visualization and image- guided intervention in medicine
    Verlag: Oxford :Univ. Press,
    Erscheinungsjahr: 1996-1999
    Erscheinungsverlauf: 1.1996/97 - 3.1999; damit Ersch. eingest.
    ISSN: 1361-8431
    Materialart: Elektronische Ressource
    Sprache: Unbestimmte Sprache
    Paralleltitel: Druckausg. ---〉:Medical image analysis
    Paralleltitel: Internetausg. ---〉:Medical image analysis
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  • 171
    Buch
    Buch
    New York, NY :ACM, ; Nachgewiesen 2.1971 - 20.1999,4; damit Ersch. eingest.
    Titel: Computer personnel : a quarterly publ. of the Special Interest Group on Computer Personnel Research, SIGCPR
    Verlag: New York, NY :ACM,
    Erscheinungsjahr: 1971-1999
    Erscheinungsverlauf: Nachgewiesen 2.1971 - 20.1999,4; damit Ersch. eingest.
    ISSN: 0160-2497
    Materialart: Buch
    Paralleltitel: Internetausg. ---〉:Computer personnel
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 172
    Zeitschrift/Serie
    Zeitschrift/Serie
    Amsterdam [u.a.] :Elsevier [u.a.], ; 9.1985 - 30.1998
    Titel: Computer networks and ISDN systems : the international journal of computer and telecommunications networking
    Verlag: Amsterdam [u.a.] :Elsevier [u.a.],
    Erscheinungsjahr: 1985-1998
    Erscheinungsverlauf: 9.1985 - 30.1998
    ISSN: 0169-7552 , 0376-5075
    Materialart: Zeitschrift/Serie
    Sprache: Unbestimmte Sprache
    Nachfolgender Titel: Vorg. u. Forts. ---〉:Computer networks
    Anmerkung: Computer networks for research in Europe
    Suppl.: In 14,1=15 von:Networkshop: Conference report
    Suppl.: 16,1/2=4; 17,4/5=5 von:European Networkshop: European Networkshop
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  • 173
    Zeitschrift/Serie
    Zeitschrift/Serie
    Woodbury, NY :AIP, ; 1.1987,1(Nov./Dez.); 2.1988 - 12.1998
    Titel: Computers in physics /
    Beteiligte Person(en): American Institute of Physics
    Verlag: Woodbury, NY :AIP,
    Erscheinungsjahr: 1987-1998
    Erscheinungsverlauf: 1.1987,1(Nov./Dez.); 2.1988 - 12.1998
    ISSN: 0894-1866
    Materialart: Zeitschrift/Serie
    Sprache: Unbestimmte Sprache
    Nachfolgender Titel: Forts. ---〉:Computing in science & engineering
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  • 174
    Zeitschrift/Serie
    Zeitschrift/Serie
    San Francisco, Calif. :Miller Freeman, ; 1.1983 - 16.1998,3
    Titel: Unix review : the publication for the Unix community
    Verlag: San Francisco, Calif. :Miller Freeman,
    Erscheinungsjahr: 1983-1998
    Erscheinungsverlauf: 1.1983 - 16.1998,3
    ISSN: 0742-3136
    Materialart: Zeitschrift/Serie
    Sprache: Unbestimmte Sprache
    Nachfolgender Titel: Forts. ---〉:Unix review's performance computing
    Paralleltitel: Internetausg. ---〉:Unix review.com
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  • 175
    Zeitschrift/Serie
    Zeitschrift/Serie
    New York, NY :ACM, ; 4.1969 - 33.1998,2; damit Ersch. eingest
    Titel: SIGNUM newsletter
    Autor: Association for Computing Machinery / Special Interest Group on Numerical Mathematics
    Verlag: New York, NY :ACM,
    Erscheinungsjahr: 1969-1998
    Erscheinungsverlauf: 4.1969 - 33.1998,2; damit Ersch. eingest
    ISSN: 0163-5778
    Materialart: Zeitschrift/Serie
    Vorheriger Titel: Vorg. ---〉:Association for Computing Machinery / Special Interest Committee on Numerical Mathematics: SICNUM newsletter
    Suppl.: 16,3=3,2 von:Association for Computing Machinery / Technical Committee on Fortran: FORTEC forum
    Paralleltitel: Internetausg. ---〉:Numerical mathematics
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  • 176
    Titel: SIGART bulletin : a quarterly publ. of the Special Interest Group on Artificial Intelligence
    Autor: Association for Computing Machinery / Special Interest Group on Artificial Intelligence
    Verlag: New York, NY :ACM,
    Erscheinungsjahr: 1990-1998
    Erscheinungsverlauf: 1.1990 - 9.1998
    ISSN: 1053-4830
    Materialart: Zeitschrift/Serie
    Sprache: Unbestimmte Sprache
    Vorheriger Titel: Vorg. ---〉:Association for Computing Machinery / Special Interest Group on Artificial Intelligence: SIGART newsletter
    Nachfolgender Titel: Forts. ---〉:Intelligence
    Paralleltitel: Internetausg. ---〉:Artificial intelligence
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  • 177
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    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3129-3140 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: The exact order reduction method solves the fourth-order system of equations from the Vlasov equations that describe mode conversion by breaking the solution into two steps. The first step is to find the numerical solutions of a pair of second-order equations for the fast waves and slow waves, respectively, which are easily obtained. The second step uses an associated integral equation to obtain the coupling between the fast and slow waves. Potential difficulties due to singularities in the kernel of the integral equations near the axis are resolved by altering the integration path. This allows accurate estimates for mode conversion efficiencies in realistic geometries as the integral equation is solved only in a narrow region near resonance, while the global fast wave solution of the reduced second-order equation covers the entire cross section. The method makes virtually no approximations except that it keeps only the lowest nontrivial order terms in the Larmor radius expansion. © 1997 American Institute of Physics.
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  • 178
    Digitale Medien
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    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3200-3203 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: It is shown that the electric field of Langmuir oscillations in a cold plasma contains a component, independent of time, setting ions in motion. Using Lagrange variables, one-dimensional dynamics of plasma in respect to the interaction between electron oscillations and ion movement is investigated. As a consequence of this interaction, the crossing of electron trajectories occurs even at small amplitudes at time tc, i.e., one-dimensional turbulence appears in the system. The expression for tc is derived. In time tc ion displacements as well as ion energy are found to depend only on the electron–ion mass relationship. © 1997 American Institute of Physics.
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  • 179
    Digitale Medien
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    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3211-3216 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: The bootstrap current in a non-Maxwellian tokamak plasma with electron cyclotron heating is calculated. The calculation is exact in the limit of highly charged ions, where pitch-angle scattering dominates over quasilinear diffusion, and shows that the current is entirely determined by the pressure of the trapped electrons. If the ion charge is finite, the current is shown to consist of two terms: one driven by collisions, and one driven by the heating and losses. The former is calculated approximately by using a model collision operator, and is found to be determined by the distribution of trapped electrons alone; the latter is discussed qualitatively.
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  • 180
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3204-3210 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Anomalous width–amplitude variations were observed in large amplitude rarefactive solitary waves which show increasing width with increasing amplitude, contrasting the usual reciprocal relation between the square of the width and the amplitude, beyond a certain value of the plasma parameters [S. S. Ghosh, K. K. Ghosh, and A. N. Sekar Iyengar, Phys. Plasmas, 3, 3939 (1996)]. For the limiting maximum amplitude, the "increasing width" solitary wave tends to a double layer-like solution. The overall variation was found to depend crucially on the specific parameter space. From a detailed investigation of the above behavior, a plausible physical explanation has been presented for such increases in the width. It is found that the ions' initial kinetic energies and the cold electron concentration within the perturbed region play a significant role in determining the observed width–amplitude variation. This contradicts the investigation of Sayal, Yadav, and Sharma [Phys. Scr. 47, 576 (1993)]. © 1997 American Institute of Physics.
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  • 181
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3254-3261 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: The aspect ratio scaling of toroidal plasma equilibria is examined using a parametrization of an exact Solov'ev solution to the Grad–Shafranov equation in Boozer coordinates. The equilibrium analysis suggests that simultaneous enhancements in magnetohydrodynamic (MHD) stability and the bootstrap effect are possible in tight aspect ratio (A→1) tokamaks. The fundamental physical mechanism causing the enhancements is shown to be the natural increase of the MHD safety factor q in tight aspect ratio toroidal geometries. The results of the scaling model suggest that the lowest bootstrap current fractions are obtained in tokamaks with aspect ratios A(approximate)3. It is also shown that a tight aspect ratio bootstrapped tokamak can be a weakly paramagnetic device. © 1997 American Institute of Physics.
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  • 182
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3282-3292 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: High resolution calculations of resistive pressure gradient-driven turbulence for the plasma edge parameters of the Advanced Toroidal Facility (ATF) [J. F. Lyon et al., Fusion Technol. 10, 179 (1986)] electron cyclotron heated discharges give fluctuation levels, consistent with the experimental measurements. This turbulence model is also used to simulate the transition from the low confinement to the high confinement mode. The transition is triggered through the poloidal flow amplification induced by the Reynolds stress. After the transition, the confinement improvement is relatively low (30%–40%), even for unrealistically low poloidal viscosity. In the high confinement mode, the characteristic radial scale length of the poloidal flow in the three-dimensional calculations (separation between the lowest-n resonant surfaces) is different from the single helicity results (radial correlation length of the fluctuations). The simple criterion based on the ratio of shearing rate to the linear growth rate does not quantitatively account for the fluctuation reduction. © 1997 American Institute of Physics.
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  • 183
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3320-3322 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Conventional neoclassical transport theory is extended to include the effects of orbit squeezing, and to allow the effective poloidal Mach number UpM=[(V(parallel)/vt)+(VEB/vtBp)] of the order of unity for incompressible tokamak plasmas. Here, V(parallel) is the parallel mass flow, vt is the ion thermal speed, VE is the poloidal E×B drift speed, B is the magnetic field strength, and Bp is the poloidal magnetic field strength. It is found that ion thermal conductivity is reduced from its conventional neoclassical value in both banana and plateau regimes if UpM〉1 and S〉1. Here, S=[1+cI2Φ′′/(Ω0B0)] is the orbit squeezing factor with c the speed of light, I=RBt, R the major radius, Φ the electrostatic potential, B0 the magnetic field strength on the axis, Ω0=eB0/Mc, M the ion mass, e the ion charge, Φ′′=d2Φ/dψ2, and ψ the poloidal flux function. However, there is an irreducible minimum for the ion thermal conductivity in the banana-plateau regime set by the conventional Pfirsch–Schlüter transport. © 1997 American Institute of Physics.
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  • 184
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3334-3340 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Ion temperature gradient (ITG or ηi) driven microinstabilities are studied, using kinetic theory, for tokamak plasmas with very weak (positive or negative) magnetic shear (VWS). The gradient of magnetic shear as well as the effects of parallel and perpendicular velocity shear (v(parallel)′ and vE′) are included in the defining equations. Two eigenmodes: the double (D) and the global (G) are found to coexist. Parametric dependence of these instabilities, and of the corresponding quasilinear transport is systematically analyzed. It is shown that, in VWS plasmas, a parallel velocity shear (PVS) may stabilize or destabilize the modes, depending on the individual as well as the relative signs of PVS and of the gradient of magnetic shear. The quasilinear transport induced by the instabilities may be significantly reduced with PVS in VWS plasmas. The vE′ values required to completely suppress the instabilities are much lower in VWS plasmas than they are in normal plasmas. Possible correlations with tokamak experiments are discussed. © 1997 American Institute of Physics.
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  • 185
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3380-3381 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: In a plasma-filled free electron laser two-stream instability is a serious consideration. The growth rate of the instability could be significantly reduced by coupling it to the electromagnetic modes/quasimodes through the wiggler. The effect is important near wiggler plasma resonance, where plasma frequency equals the product of wiggler wave number and beam velocity. © 1997 American Institute of Physics.
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  • 186
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3390-3393 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Stimulated emission from the interaction of a cold, relativistic beam of electrons gyrating in a combined solenoidal and longitudinally polarized periodic wiggler magnetic field is considered as a source of high-efficiency and short-wavelength radiation. The analysis of electron motion in such a combined field shows the motion covers rich Fourier components. The first Fourier component, with the cyclotron frequency of ωc+kwv(parallel), has relatively large transverse velocity compared with the velocity of the motion. The study of the interaction of this Fourier component with the peniotron electromagnetic mode indicates that a high efficiency of 36% is obtained. Its working mechanism is explained and the influence of the wiggler field on the saturation efficiency is analyzed. The electron bunching in the transverse plane and the evolution of the efficiency with the interaction distance is given.
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  • 187
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2785-2787 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: By solving the dispersion relation in the ion kinetic regime, it is found that the threshold of the plasma beta value for exciting the ion-fishbone mode is lowered. Thus, for most of the present-day tokamaks where the Bussac criterion [Bussac et al., Phys. Rev. Lett. 35, 1638 (1975)] is not satisfied, it will still be possible to excite the ion-fishbone mode. © 1997 American Institute of Physics.
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  • 188
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2788-2790 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: An approach of producing the poloidal ion rotation by using ion cyclotron resonance heating (ICRH) is presented in core tokamak plasmas. The mechanism employed here is inducing a poloidal density inhomogeneity by rf cyclotron heating and then destabilizing the anomalous Stringer spin-up. A criterion for destabilization of the poloidal ion rotation in the presence of a rf wave is given, which depends on the ratio of the characteristic time of inhomogeneous density formation to the ion collision time. The numerical results have shown that the poloidal ion rotation can be destabilized in the present ICRH power level. © 1997 American Institute of Physics.
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  • 189
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2893-2898 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Experiments on the excitation of rarefactive ion acoustic solitons using a fine mesh grid in a negative ion plasma are described. The excitation is novel in that a modulated high-frequency sinusoidal wave voltage signal is applied to the grid. An interpretation of the velocity modulation and bunching of free-streaming ions that pass through the grid to which the signal is applied is given. © 1997 American Institute of Physics.
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  • 190
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2907-2919 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: In general, turbulent transport drives a plasma toward a state of turbulent equipartition, in which Lagrangian invariants are uniformly distributed. Different invariants decay with different rates, and in tokamaks the frozen-in law of particles in the poloidal magnetic field survives longer than the corresponding law for the toroidal field, assuming that the trapped particles dominate the turbulent transport. Therefore, the plasma profiles depend on the safety factor q(r), and the condition for convection of trapped particles is that the shear dq/dr is positive. There are two ways to suppress this convection and thereby enhance confinement. The first one is to reverse the magnetic shear. The energy of typical trapped particles then increases outward instead of inward, which suppresses instabilities. The second method is to eliminate the trapped ions by poloidal rotation, and thereby create a transport barrier. © 1997 American Institute of Physics.
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  • 191
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2933-2939 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: A feedback control system using an ion beam as a remote suppressor has been previously shown to be very effective in suppressing plasma instabilities in the Columbia Linear Machine [G. A. Navratil et al., Plasma Phys. 24, 184 (1982)]. The first experimental measurements for the effect of this feedback system on anomalous particle transport, as determined from the cross-correlation of density and potential fluctuations is presented. It is shown that feedback reduces transport due to a rotational E×B mode by up to a factor of 3 in this experiment. Also, it was found that particle transport scales linearly with fluctuation amplitude and feedback control does not alter this scaling. Last, the experimentally observed scaling of particle transport does not agree with any theoretical predictions. © 1997 American Institute of Physics.
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  • 192
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2955-2961 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: In this paper we present results related to studies of low frequency electrostatic fluctuations in a toroidal plasma of varying length and without a toroidal current. The toroidal length of plasma is varied from fully toroidal (major radius R=45 cm) to 278, 212 and 142 cm. The characteristics of fluctuations changed, showing the effect of finite system length on the nature of the fluctuations. The major results are (1) a drastic reduction in the amplitude of fluctuations, (2) this reduction is mainly due to the disappearance of coherent peaks at 3 kHz and its harmonics observed in unbounded system, (3) the presence of a broad coherent feature around 10 kHz, only in bad curvature region, at low magnetic field (200 G) and (4) the appearance of a large number of coherent peaks, in one particular system length, at a higher magnetic field (400 G). These results indicate that the Rayleigh–Taylor instability with finite k|| may be excitable in the device. © 1997 American Institute of Physics.
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  • 193
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2989-2996 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Thomson scattering measurements performed in the divertor of the DIII-D tokamak [Plasma Physics Controlled Nuclear Fusion Research, 1986 (International Atomic Energy Agency, Vienna, 1987), Vol. I, p. 159] during detached operation show that the electron temperatures are typically between 0.8 and 2.0 eV throughout a region which may extend several centimeters above the target plate. At such low temperatures the excitation of recycling deuterium atoms or impurities should be weak. Nevertheless, significant radiation is frequently detected in these locations. It has been suggested that recombination processes, which become important only below about 1.5 eV for deuterium, are responsible for the observed emission. This hypothesis has been investigated by comparing ratios of deuterium lines from attached and detached plasmas with theoretical ratios expected for ionizing or recombining conditions. The analysis of several discharges indicates that the mechanism for production of the emission changes from being collisional excitation of atomic deuterium to a mixture of collisional-radiative recombination and collisional excitation as plasmas evolve from attached to detached states. Localization of D-α emission to low-temperature regions using tangentially viewing camera data together with Thomson scattering results and measurements of deuterium atom temperatures are consistent with these conclusions. © 1997 American Institute of Physics.
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  • 194
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3006-3011 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: In an experiment relevant to the fast ignitor fusion concept, a preformed plasma simulating the corona of a fusion target has been probed with laser intensities exceeding 1018 W/cm2. It is seen that the f number of the probe beam is increased as it propagates through the target plasma—a channeling of the power. The transmission and backscatter of the probe beam have been examined, and the analysis suggests anomalous absorption of laser light in shorter scale length plasmas. © 1997 American Institute of Physics.
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  • 195
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3021-3030 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Absorption-spectroscopy measurements using an embedded titanium layer have been performed on laser implosions of spherical shells. Predicted absorption features formed by the titanium layer were observed: absorption lines due to 1s–2p transitions in titanium ions of incomplete L shell, as well as K-edge absorption in cold titanium. Also observed were oscillations due to EXAFS (Extended X-Ray Absorption Fine Structure) above the Ti K edge. The core temperature and shell areal density and temperature are derived from the measurements and are found to fall short of the values predicted by one-dimensional code simulations. This shortfall is attributed to the lack of irradiation symmetry, which leads to hydrodynamic instability and mixing (smoothing by phase plates was not used in this experiment). Signatures of mixing include the emission of the He-α line of Ti+20 due to titanium migrating to the core, as well as the EXAFS spectrum indicating cold titanium close to peak compression.
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  • 196
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 3043-3048 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Extensive simulations are performed to investigate effects of electron cyclotron instabilities on the gyrotron beam quality, using two-dimensional axisymmetric particle-in-cell (PIC) codes. Both electrostatic and electromagnetic models, as well as realistic geometries of the gyrotron, are considered. It is found that a large beam density can lead to an electrostatic-instability-induced energy spread which substantially degrades the gyrotron efficiency. © 1997 American Institute of Physics.
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  • 197
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2313-2315 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: A self-consistent, two-dimensional analysis is presented on confining a region of neutral plasma with a Penning/Malmberg type plasma trap using a nested well configuration. It is found that a neutral plasma region having disparate electron and ion temperatures or having high charge state ions can be confined with static fields. For confining a neutral region comprised of electrons and equal temperature low charge state ions, a quasistatic approach appears promising. © 1997 American Institute of Physics.
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  • 198
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2322-2330 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: The Vlasov fluid model is used to study the m=0 and m=1 internal and free boundary modes in a collisionless, large Larmor radius Z pinch. Two methods (initial value and variational) are employed, and give good agreement. The growth rate can be reduced from its zero Larmor radius value by a factor of up to 10 for m=1, and up to 3 for m=0. Stability thresholds and the role of resonant ions are discussed. © 1997 American Institute of Physics.
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  • 199
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2336-2347 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Based on the resolution of the partial differential equation describing the external excitation of the Bohm–Gross longitudinal wave, analytical expressions for causal responses of a dissipative macroscopic plasma are derived. Both impulsive and harmonic solutions representing the spatial Green's functions of the radiation problem are given. These exact responses of the plasma, expressed in terms of two-variable Lommel functions, are then used to gain some better understanding of the excitation and dynamics of the well-known thermal wave. Special attention is paid to the resonant excitation case. Intrinsic characteristics of the secular behavior of the radiated signal are illustrated and analyzed. It is shown that the proffered algebraic solutions constitute a generalization of previous results inferred from an asymptotic representation of the Green's functions, or from the familiar steady state harmonic approach. © 1997 American Institute of Physics.
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  • 200
    Digitale Medien
    Digitale Medien
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 4 (1997), S. 2436-2442 
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik
    Notizen: Experiments on the excitation of ion acoustic solitons using a fine mesh grid in a normal two component plasma are described. The excitation is novel in that a modulated high-frequency sinusoidal wave voltage signal is applied to the grid. The carrier frequency of the high-frequency sinusoidal wave is above the ion plasma frequency. An interpretation of the velocity modulation and bunching of free streaming ions that pass through the grid to which the signal is applied is given. © 1997 American Institute of Physics.
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