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Year
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  • 101
    Publication Date: 2021-08-03
    Language: English
    Type: article , doc-type:article
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  • 102
    Publication Date: 2021-03-05
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 103
    Publication Date: 2021-10-28
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 104
    Publication Date: 2020-09-14
    Language: English
    Type: article , doc-type:article
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  • 105
    Publication Date: 2021-04-16
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 106
    Publication Date: 2021-02-23
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 107
    Publication Date: 2021-03-26
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 108
    Publication Date: 2021-02-23
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 109
    Publication Date: 2022-03-14
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 110
    Publication Date: 2021-02-22
    Language: English
    Type: bookpart , doc-type:bookPart
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  • 111
    Publication Date: 2022-03-14
    Description: 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.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 112
    Publication Date: 2021-02-05
    Language: English
    Type: article , doc-type:article
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  • 113
    Publication Date: 2022-03-14
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 114
    Publication Date: 2021-04-20
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 115
    Publication Date: 2021-07-06
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 116
    Publication Date: 2021-02-23
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 117
    Publication Date: 2021-10-26
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 118
  • 119
    Publication Date: 2022-06-13
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 120
    Publication Date: 2022-06-13
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 121
    Publication Date: 2022-06-13
    Language: English
    Type: masterthesis , doc-type:masterThesis
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  • 122
    Publication Date: 2022-06-13
    Language: English
    Type: article , doc-type:article
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  • 123
    Publication Date: 2022-06-13
    Language: English
    Type: article , doc-type:article
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  • 124
  • 125
    Publication Date: 2022-06-13
    Language: English
    Type: researchdata , doc-type:ResearchData
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  • 126
    Publication Date: 2022-06-13
    Description: 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.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 127
    Publication Date: 2022-06-13
    Language: English
    Type: article , doc-type:article
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  • 128
    Publication Date: 2022-06-13
    Language: English
    Type: other , doc-type:Other
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  • 129
    Publication Date: 2022-06-27
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 130
    Publication Date: 2022-06-27
    Language: English
    Type: article , doc-type:article
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  • 131
    Publication Date: 2022-06-27
    Description: 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.
    Language: English
    Type: bookpart , doc-type:bookPart
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  • 132
    Publication Date: 2022-07-07
    Language: English
    Type: bookpart , doc-type:bookPart
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  • 133
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 134
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 135
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 136
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
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  • 137
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: other , doc-type:Other
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  • 138
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
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  • 139
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: conferenceobject , doc-type:conferenceObject
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  • 140
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 141
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
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  • 142
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
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  • 143
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
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  • 144
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 145
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 146
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 147
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 148
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 149
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 150
    Publication Date: 2022-07-19
    Language: English
    Type: article , doc-type:article
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  • 151
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 152
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 153
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 154
    Publication Date: 2022-07-19
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 155
    Publication Date: 2022-09-22
    Description: 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.
    Language: English
    Type: researchdata , doc-type:ResearchData
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  • 156
    Publication Date: 2022-11-28
    Language: English
    Type: book , doc-type:book
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  • 157
  • 158
    Publication Date: 2022-11-28
    Language: English
    Type: incollection , doc-type:Other
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  • 159
    Publication Date: 2022-11-28
    Description: 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.
    Language: English
    Type: article , doc-type:article
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  • 160
    Publication Date: 2022-11-28
    Description: 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.
    Language: German
    Type: book , doc-type:book
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  • 161
    Publication Date: 2022-11-28
    Language: English
    Type: incollection , doc-type:Other
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  • 162
    Publication Date: 2022-11-28
    Description: 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.
    Language: English
    Type: reportzib , doc-type:preprint
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  • 163
    Publication Date: 2022-12-05
    Language: English
    Type: article , doc-type:article
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  • 164
    Unknown
    London ; New York : Taylor & Francis
    Keywords: Fluid mechanics.
    Pages: x, 696 p.
    Edition: 8th ed
    ISBN: 0-203-01232-1
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  • 165
    Unknown
    London ; New York : Taylor & Francis
    Keywords: Canals, Design and construction. ; Canals, Maintenance and repair.
    Pages: xx, 389 p.
    ISBN: 0-203-01242-9
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  • 166
    Unknown
    Hershey, PA : Idea Group Pub
    Keywords: Electronic books ; Internet marketing
    Pages: 1 v. (various pagings)
    ISBN: 1-591-40826-1
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  • 167
    Unknown
    Abingdon [England] ; New York : Taylor & Francis
    Keywords: Courtyard houses.
    Pages: xix, 248 p., [8] p. of plates
    ISBN: 0-203-64672-X
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  • 168
    Keywords: Electronic books ; Electronic commerce, Management ; Information technology, Management ; Technological innovations, Management
    Pages: 1 v. (various pagings)
    ISBN: 1-591-40631-5
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  • 169
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 63-96 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Helicobacter pylori is the main cause of peptic ulceration, distal gastric adenocarcinoma, and gastric lymphoma. Only 15% of those colonized develop disease, and pathogenesis depends upon strain virulence, host genetic susceptibility, and environmental cofactors. Virulence factors include the cag pathogenicity island, which induces proinflammatory, pro-proliferative epithelial cell signaling; the cytotoxin VacA, which causes epithelial damage; and an adhesin, BabA. Host genetic polymorphisms that lead to high-level pro-inflammatory cytokine release in response to infection increase cancer risk. Pathogenesis is dependent upon inflammation, a Th-1 acquired immune response and hormonal changes including hypergastrinaemia. Antral-predominant inflammation leads to increased acid production from the uninflamed corpus and predisposes to duodenal ulceration; corpus-predominant gastritis leads to hypochlorhydria and predisposes to gastric ulceration and adenocarcinoma. Falling prevalence of H. pylori in developed countries has led to a falling incidence of associated diseases. However, whether there are disadvantages of an H. pylori-free stomach, for example increased risk of esosphageal adenocarcinoma, remains unclear.
    Type of Medium: Electronic Resource
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  • 170
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 435-466 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Sarcomas form a highly diverse group of rare tumors that are derived from connective tissue. More than 100 different malignant and benign soft tissue neoplasms can be recognized by histologic examination. Few diagnostic markers exist, and the cell of origin for many soft tissue tumors is unknown. The accurate diagnosis of many of these tumors therefore remains a challenge. The study of sarcomas has yielded many insights that can be applied to other neoplasms such as carcinoma. For example, the success of the treatment of gastrointestinal stromal tumor with Imatinib has led to an increased effort to find targeted therapies for other malignancies. Here we describe the known molecular changes in a number of sarcomas and focus on novel scientific approaches that can be expected to lead to improved diagnosis, prognostication, and therapy of sarcoma.
    Type of Medium: Electronic Resource
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  • 171
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 225-249 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The gas-lift technique comprises the injection of gas bubbles in vertical oil wells to increase production. It is based on a reduction of the tubing gravitational pressure gradient. Several fluid-flow phenomena influencing such vertical gas-liquid flows are discussed. These effects include the radial distribution of void fraction and of gas and liquid velocity, flow regime changes, and system stability problems. Associated consequences for gas-lift performance and related optimization approaches are also discussed.
    Type of Medium: Electronic Resource
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  • 172
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 193-224 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: What mechanisms of flow control do animals use to enhance hydrodynamic performance? Animals are capable of manipulating flow around the body and appendages both passively and actively. Passive mechanisms rely on structural and morphological components of the body (i.e., humpback whale tubercles, riblets). Active flow control mechanisms use appendage or body musculature to directly generate wake flow structures or stiffen fins against external hydrodynamic loads. Fish can actively control fin curvature, displacement, and area. The vortex wake shed by the tail differs between eel-like fishes and fishes with a discrete narrowing of the body in front of the tail, and three-dimensional effects may play a major role in determining wake structure in most fishes.
    Type of Medium: Electronic Resource
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  • 173
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 395-425 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.
    Type of Medium: Electronic Resource
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  • 174
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 309-338 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Electrophoretic separation of a mixture of chemical species is a fundamental technique of great usefulness in biology, health care, and forensics. In capillary electrophoresis (which has evolved from its predecessor, slab-gel electrophoresis), the sample migrates through a single microcapillary instead of through the network of pores in a gel. A fundamental design problem is to minimize dispersion in the separation direction. Molecular diffusion is inevitable and sets a theoretical limit on the best separation that can be achieved. But in practice, there are a number of effects arising out of the interplay between fluid flow, chemistry, thermal effects, and electric fields that result in enhanced dispersion. This paper reviews the subject of fluid flow in such capillary microchannels and examines the various causes of enhanced dispersion that limit the efficiency of separation.
    Type of Medium: Electronic Resource
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  • 175
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 27-63 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Race car performance depends on elements such as the engine, tires, suspension, road, aerodynamics, and of course the driver. In recent years, however, vehicle aerodynamics gained increased attention, mainly due to the utilization of the negative lift (downforce) principle, yielding several important performance improvements. This review briefly explains the significance of the aerodynamic downforce and how it improves race car performance. After this short introduction various methods to generate downforce such as inverted wings, diffusers, and vortex generators are discussed. Due to the complex geometry of these vehicles, the aerodynamic interaction between the various body components is significant, resulting in vortex flows and lifting surface shapes unlike traditional airplane wings. Typical design tools such as wind tunnel testing, computational fluid dynamics, and track testing, and their relevance to race car development, are discussed as well. In spite of the tremendous progress of these design tools (due to better instrumentation, communication, and computational power), the fluid dynamic phenomenon is still highly nonlinear, and predicting the effect of a particular modification is not always trouble free. Several examples covering a wide range of vehicle shapes (e.g., from stock cars to open-wheel race cars) are presented to demonstrate this nonlinear nature of the flow field.
    Type of Medium: Electronic Resource
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  • 176
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 453-482 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Large-eddy simulation (LES) of turbulent combustion is a relatively new research field. Much research has been carried out over the past years, but to realize the full predictive potential of combustion LES, many fundamental questions still have to be addressed, and common practices of LES of nonreacting flows revisited. The focus of the present review is to highlight the fundamental differences between Reynolds-averaged Navier-Stokes (RANS) and LES combustion models for nonpremixed and premixed turbulent combustion, to identify some of the open questions and modeling issues for LES, and to provide future perspectives.
    Type of Medium: Electronic Resource
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  • 177
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 371-394 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Mammalian fertilization requires the coordinated activity of motile spermatozoa, muscular contractions of the uterus and oviduct, as well as ciliary beating. These elastic structures generate forces that drive fluid motion, but their configurations are, in turn, determined by the fluid dynamics. We review the basic fluid mechanical aspects of reproduction, including flagellar/ciliary beating and peristalsis. We report on recent biological studies that have shed light on the relative importance of the mechanical ingredients of reproduction. In particular, we examine sperm motility in the reproductive tract, ovum pickup and transport in the oviduct, as well as sperm-egg interactions. We review recent advances in understanding the internal mechanics of cilia and flagella, flagellar surface interaction, sperm motility in complex fluids, and the role of fluid dynamics in embryo transfer. We outline promising computational fluid dynamics frameworks that may be used to investigate these complex, fluid-structure interactions.
    Type of Medium: Electronic Resource
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  • 178
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 483-512 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: This article provides a critical review of computational techniques for flow-noise prediction and the underlying theories. Hybrid approaches, in which the turbulent noise source field is computed and/or modeled separately from the far-field calculation, are afforded particular attention. Numerical methods and modern flow simulation techniques are discussed in terms of their suitability and accuracy for flow-noise calculations. Other topics highlighted include some important formulation and computational issues in the application of aeroacoustic theories, generalized acoustic analogies with better accounts of flow-sound interaction, and recent computational investigations of noise-control strategies. The review ends with an analysis of major challenges and key areas for improvement in order to advance the state of the art of computational aeroacoustics.
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  • 179
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 129-157 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The challenges in understanding hypersonic flight are discussed and critical hypersonic aerothermodynamics issues are reviewed. The ability of current analytical methods, numerical methods, ground testing capabilities, and flight testing approaches to predict hypersonic flow are evaluated. The areas where aerothermodynamic shortcomings restrict our ability to design and analyze hypersonic vehicles are discussed, and prospects for future capabilities are reviewed. Considerable work still needs to be done before our understanding of hypersonic flow will allow for the accurate prediction of vehicle flight characteristics throughout the flight envelope from launch to orbital insertion.
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  • 180
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 277-307 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: We review mathematical models of confined bubbles, emphasizing physical mechanisms as expressed in simple geometries. Molecular interactions between liquid, gas, and the confining solid are all important and are described through the disjoining pressure concept. Methods for finding static shapes are considered. The static solution is a springboard for discussing pressure-driven and surface-tension-driven flows, both of which involve viscous effects and macroscopic films entrained near apparent contact lines. We next discuss vapor bubbles produced by thermal effects. Vaporization localized near contact lines and condensation distributed in colder parts of the interface lead to steady vapor bubbles. Their size is determined through global constraints. Unsteady vapor bubbles are discussed and we end with thoughts on open problems.
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  • 181
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Fluid Mechanics 38 (2006), S. 159-192 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The review deals with drop impacts on thin liquid layers and dry surfaces. The impacts resulting in crown formation are referred to as splashing. Crowns and their propagation are discussed in detail, as well as some additional kindred, albeit nonsplashing, phenomena like drop spreading and deposition, receding (recoil), jetting, fingering, and rebound. The review begins with an explanation of various practical motivations feeding the interest in the fascinating phenomena of drop impact, and the above-mentioned topics are then considered in their experimental, theoretical, and computational aspects.
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 405-434 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Loss of Ca2+ homeostasis, often in the form of cytoplasmic increases, leads to cell injury. Depending upon cell type and the intensity of Ca2+ toxicity, the ensuing pathology can be reversible or irreversible. Although multiple destructive processes are activated by Ca2+, lethal outcomes are determined largely by Ca2+-induced mitochondrial permeability transition. This form of damage is primarily dependent upon mitochondrial Ca2+ accumulation, which is regulated by the mitochondrial membrane potential. Retention of the mitochondrial membrane potential during Ca2+ increases favors mitochondrial Ca2+ uptake and overload, resulting in mitochondrial permeability transition and cell death. In contrast, dissipation of mitochondrial membrane potential reduces mitochondrial Ca2+ uptake, retards mitochondrial permeability transition, and delays death, even in cells with large Ca2+ increases. The rates of mitochondrial membrane potential dissipation and mitochondrial Ca2+ uptake may determine cellular sensitivity to Ca2+ toxicity under pathological conditions, including ischemic injury.
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  • 183
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 297-329 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Atherosclerosis, the cause of myocardial infarction, stroke, and ischemic gangrene, is an inflammatory disease. The atherosclerotic process is initiated when cholesterol-containing low-density lipoproteins accumulate in the intima and activate the endothelium. Leukocyte adhesion molecules and chemokines promote recruitment of monocytes and T cells. Monocytes differentiate into macrophages and upregulate pattern recognition receptors, including scavenger receptors and toll-like receptors. Scavenger receptors mediate lipoprotein internalization, which leads to foam-cell formation. Toll-like receptors transmit activating signals that lead to the release of cytokines, proteases, and vasoactive molecules. T cells in lesions recognize local antigens and mount T helper-1 responses with secretion of pro-inflammatory cytokines that contribute to local inflammation and growth of the plaque. Intensified inflammatory activation may lead to local proteolysis, plaque rupture, and thrombus formation, which causes ischemia and infarction. Inflammatory markers are already used to monitor the disease process and anti-inflammatory therapy may be useful to control disease activity.
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  • 184
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 119-150 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: In the past 25 years, a majority of cancer studies have focused on examining functional consequences of activating and/or inactivating mutations in critical genes implicated in cell cycle control. These studies have taught us a great deal about the functions of oncogenes and tumor suppressor genes and the signaling pathways regulating cell proliferation and/or cell death. However, such studies have largely ignored the fact that cancers are heterogeneous cellular entities whose growth is dependent upon reciprocal interactions between genetically altered "initiated" cells and the dynamic microenvironment in which they live. This review highlights the aspects of cancer development that, like organogenesis during embryonic development and tissue repair in adult mammals, are regulated by interactions between epithelial cells, activated stromal cells, and soluble and insoluble components of the extracellular matrix.
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  • 185
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 243-271 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Prostate cancer displays considerable clinical, morphological, and biological heterogeneity. Classical genetic techniques have provided only limited information about the pathogenesis of prostate cancer progression. Nevertheless, several candidate genes and pathways have been implicated in prostate cancer development. High-throughput techniques have exponentially expanded the number of candidate genes, including some whose role in prostate cancer pathogenesis has been studied. However, the techniques used to study the prostate cancer genome, transcriptome, and proteome generate massive amounts of data that have yet to be integrated and explored. To move beyond candidate gene identification and develop a comprehensive understanding of cancer pathogenesis, integrative approaches need to analyze this data on a global level. This review addresses candidate genes involved in prostate cancer pathogenesis in a biological and clinical context and demonstrates how integrated analysis of high-throughput data augments our understanding of prostate cancer.
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  • 186
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 349-374 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Nonimmune glomerulopathies are an area of significant research. This review discusses the development of focal segmental glomerulosclerosis, with particular attention to the role of the podocyte in the initiation of glomerulosclerosis and the contribution to glomerulosclerosis from capillary hypertension and soluble factors such as transforming growth factor beta, platelet-derived growth factor, vascular endothelial growth factor, and angiotensin. The effects of these factors on endothelial and mesangial cells are also discussed. In addition, we review our current understanding of the slit diaphragm (a specialized cell junction found in the kidney), slit diaphragmĐ??associated proteins (including nephrin, podocin, ʼ̛-actinin-4, CD2-associated protein, and transient receptor potential channel 6), and the role of these proteins in glomerular disease. We also discuss the most recent research on the pathogenesis of collapsing glomerulosclerosis, human immunodeficiency virus associated nephropathy, Denys-Drash, diabetic nephropathy, Alport syndrome, and other diseases related to the interaction between the podocyte and the glomerular basement membrane.
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  • 187
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 97-117 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Malignant gliomas, the most common type of primary brain tumor, are a spectrum of tumors of varying differentiation and malignancy grades. These tumors may arise from neural stem cells and appear to contain tumor stem cells. Early genetic events differ between astrocytic and oligodendroglial tumors, but all tumors have an initially invasive phenotype, which complicates therapy. Progression-associated genetic alterations are common to different tumor types, targeting growth-promoting and cell cycle control pathways and resulting in focal hypoxia, necrosis, and angiogenesis. Knowledge of malignant glioma genetics has already impacted clinical management of these tumors, and researchers hope that further knowledge of the molecular pathology of malignant gliomas will result in novel therapies.
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  • 188
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 215-242 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Modern techniques of cell and molecular biology have rapidly uncovered the mechanisms underlying inflammatory injury of the lung. This expanding knowledge (which includes an understanding of complement, cell surface receptors, cytokines and chemokines, transcription factors, oxidants, proteinases, and endogenous inhibitors, as well as the role of leukocyte adhesion-promoting molecules) has provided new insights into the inflammatory system in general, as well as in the context of lung injury. In this review, we summarize recent progress in understanding the regulation of lung inflammation by using immunoglobulin G (IgG) immune complexĐ??induced lung injury as a model. These studies have provided information on the role of various inflammatory mediators and their sequence of engagement. Insights into potential interventional approaches for the suppression of inflammatory processes in humans have emerged from those studies.
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  • 189
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 375-404 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: The association between Epstein-Barr virus (EBV) and a large number of benign and malignant diseases is unique among DNA viruses. Within infected tissues, proteins that are expressed during the normal lytic and latent viral life cycle lead to cellular alterations that contribute to these EBV-associated diseases. Although the early events of EBV infection are poorly understood, increasing knowledge of the viral processes that govern viral latency has shed light upon the potential mechanisms by which EBV infection can lead to cellular transformation. Our current understanding of the role of EBV in the development of Burkitt lymphoma, Hodgkin lymphoma, nasopharyngeal carcinoma, and other EBV-associated diseases is discussed.
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 171-198 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: The endothelial cells lining vascular and lymphatic vessels are targets of several infectious agents, including viruses and bacteria, that lead to dramatic changes in their functions. Understanding the pathophysiological mechanisms that cause the clinical manifestations of those infections has been advanced through the use of animal models and in vitro systems; however, there are also abundant studies that explore the consequences of endothelial infection in vitro without supporting evidence that endothelial cells are actual in vivo targets of infection in human diseases. This article defines criteria for considering an infection as truly endothelium-targeted and reviews the literature that offers insights into the pathogenesis of human endothelial-target infections.
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 151-170 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Neurodegenerative diseases as diverse as Alzheimer's, Parkinson's, and Creutzfeldt-Jakob disease share a common pathogenetic mechanism involving aggregation and deposition of misfolded proteins, which leads to progressive central nervous system disease. Although the type of aggregated protein and the regional and cellular distribution of deposition vary from disease to disease, these disorders may all be linked by similar pathways of protein aggregation with fibril formation and amyloid deposition. This perspective on pathogenesis suggests that a wide variety of neurodegenerative diseases can be grouped mechanistically as brain amyloidoses, an outlook that yields novel insights into potential therapeutic approaches that may be applicable across the broad spectrum of neurodegenerative disease.
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 467-496 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Although Gram-negative bacteria have often been implicated in the pathogenesis of severe sepsis and septic shock, how they trigger these often lethal syndromes is uncertain. In particular, the role played by blood-borne bacteria is controversial. This review considers two alternatives. In the first, circulating Gram-negative bacteria induce toxic reactions directly within the vasculature; in the second, the major inflammatory stimulus occurs in local extravascular sites of infection and circulating bacteria contribute little to inducing toxic responses. Evidence for each alternative is found in the literature. Bacteremia and severe sepsis are not so closely linked that the most striking cases can be a model for the rest. Intravascular and extravascular triggers may warrant different approaches to prevention and therapy.
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 1-22 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: I am honored to write the prefatory chapter for the inaugural volume of the Annual Review of Pathology: Mechanisms of Disease. This publishing venture signals that pathology takes its rightful place alongside the other biomedical sciences. I thought it may be of interest to some to delineate how a circuitous path led me into a career in experimental pathology and to give some of the flavor of a past era in experimental approaches. Thus, my title.
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 331-348 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: From histological and biological perspectives, lung cancer is a complex neoplasm. Although the sequential preneoplastic changes have been defined for centrally arising squamous carcinomas of the lung, they have been poorly documented for the other major forms of lung cancers, including small cell lung carcinoma and adenocarcinomas. There are three main morphologic forms of preneoplastic lesions recognized in the lung: squamous dysplasias, atypical adenomatous hyperplasia, and diffuse idiopathic pulmonary neuroendocrine cell hyperplasia. However, these lesions account for the development of only a subset of lung cancers. Several studies have provided information regarding the molecular characterization of lung preneoplastic changes, especially for squamous cell carcinoma. These molecular changes have been detected in the histologically normal and abnormal respiratory epithelium of smokers. Two different molecular pathways have been detected in lung adenocarcinoma pathogenesis: smoking-associated activation of RAS signaling, and nonsmoking-associated activation of EGFR signaling; the latter is detected in histologically normal respiratory epithelium.
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 497-536 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Parasitic diseases represent major global health problems of immense proportion. Schistosomiasis, malaria, leishmaniasis, Chagas disease, and African sleeping sickness affect hundreds of millions of people worldwide, cause millions of deaths annually, and present an immense social and economic burden. Recent advances in genomic analysis of several of the major global parasites have revealed key factors involved in the pathogenesis of parasite diseases. Among the major virulence factors identified are parasite-derived proteases. This review focuses on the direct role of proteases in disease pathogenesis. Well-characterized examples of the roles proteases play in pathogenesis include their involvement in invasion of the host by parasite migration through tissue barriers, degradation of hemoglobin and other blood proteins, immune evasion, and activation of inflammation.
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    Annual Review of Pathology: Mechanisms of Disease (2006) 1 (2006), S. 273-296 
    ISSN: 1553-4006
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine
    Notes: Kaposi's sarcoma (KS) has long been suspected of having an infectious etiology on the basis of its unusual epidemiology, histopathology, and natural history. Nearly a decade ago, a novel herpesviral genome was discovered in KS biopsies, and since that time strong epidemiologic evidence has accumulated correlating infection with this KS-associated herpesvirus (KSHV, also known as human herpesvirus 8) with the development of the disease. Here we review the evidence linking KSHV infection to KS risk and discuss current notions of how KSHV gene expression promotes the development of this remarkable neoplasm. These studies show that both latent and lytic viral replicative cycles contribute significantlyĐ??but differentlyĐ??to KS development. The studies also highlight mechanistic differences between oncogenesis caused by KSHV and that caused by its distant relative Epstein-Barr virus.
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    Annual Review of Fluid Mechanics 38 (2006), S. 251-276 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: We review recent advances in understanding, modeling, and controlling oscillations in the flow past a cavity. The fundamental mechanisms underlying cavity flow oscillations have been known for at least 40 years, but suppressing these oscillations in a reliable and robust way is still a challenge today. Interest in controlling the flow past a cavity is motivated by aerospace applications, but in addition, cavity flows provide an attractive canonical problem for exploring general flow control techniques. The focus is on recent advances in modeling these flows, and in controlling them, using both open-loop and closed-loop techniques. A relatively new perspective is that cavity oscillations may not always be self-sustained, but under some flow conditions may be lightly damped resonances, sustained by external disturbances such as boundary layer turbulence. Areas in which our understanding is incomplete, and which deserve further study, are discussed, in particular the effects of high-frequency open-loop forcing, fundamental limitations of feedback control for a given configuration of sensors and actuators, and the development of a feedback design methodology that respects the limited range of validity of the available dynamical models.
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    Annual Review of Fluid Mechanics 38 (2006), S. 427-452 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: When the free surfaces of most solids approach their bulk melting temperatures from below, the molecular structure of the material gives way to a disordered structure with some attributes of both the solid and liquid phases. When the temperature is sufficiently close to that of bulk transition, the surface melts and literally flows as a viscous fluid. This phenomenon, called interfacial premelting, lies at the heart of the microscopic theory of melting of solid matter, and captures the interest of condensed matter physicists and physical chemists alike. The process is ubiquitous and responsible for a wide range of consequences in materials with biological, geophysical, and technological significance. Because such systems are often exposed to spatial or temporal variations in thermodynamic forcing, there are a host of fluid mechanical phenomena that result from this underlying melting behavior. The fluid dynamics of unfrozen surfaces holds clues for understanding the bulk behavior of polycrystalline materials, from Earth's mantle to the stratosphere and beyond. In this review we focus on the fluid dynamical consequences of the premelting of solids.
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    Annual Review of Fluid Mechanics 38 (2006), S. 339-369 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: We consider the hydrodynamics of creatures capable of sustaining themselves on the water surface by means other than flotation. Particular attention is given to classifying water walkers according to their principal means of weight support and lateral propulsion. The various propulsion mechanisms are rationalized through consideration of energetics, hydrodynamic forces applied, or momentum transferred by the driving stroke. We review previous research in this area and suggest directions for future work. Special attention is given to introductory discussions of problems not previously treated in the fluid mechanics literature, with hopes of attracting physicists, applied mathematicians, and engineers to this relatively unexplored area of fluid mechanics.
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    Berkeley, Calif. : Berkeley Electronic Press (now: De Gruyter)
    Journal of homeland security and emergency management 3 (2006), S. 5 
    ISSN: 1547-7355
    Source: Berkeley Electronic Press Academic Journals
    Topics: Political Science , Sociology
    Notes: There has been a recent government-wide effort to examine the nation's language needs for both the purposes of security and to increase general cultural awareness. Recent surveys of government agencies have shown that more than 80 agencies require some sort of foreign language capability to complete their missions. These surveys were, however, completed before the Department of Homeland Security (DHS) stood up, and while there may be great need for foreign language capabilities in DHS, such as in their border patrol or customs duties, that need has not been fully documented. An assessment of DHS language needs would provide information about current and future needs and would allow the department to properly implement procedures to alleviate any problems. Potential language needs are discussed and several recommendations are made to DHS so that they could work to maintain their language capabilities, rather than fall behind.
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