bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Matching and Proportional Laws of Cybernetic Models
Authors: Young Jamey D. , Ramkrishna Doraiswami 
Published: December 2006

AbstractThe Matching and Proportional Laws are heuristic control policies that have found widespread use in cybernetic models of biological systems. Within this context, the laws serve as optimization surrogates for predicting the response of metabolic control circuits that modulate enzyme levels and activities. The key result of the current contribution is to demonstrate clearly the optimality properties of these laws and the assumptions that underlie their development. In doing so, we arrive at generalized versions of the Matching and Proportional Laws that are shown to collapse to the forms originally derived by Kompala et al. ( Biotechnol. Bioeng. 1986, 28, 1044–1055) when certain simplifications are applied. As a further line of investigation, we show how Kompala et al.apos;s cybernetic laws compare with alternative control policies in their ability to describe diauxic growth behavior of microbial cultures. We find that Kompala et al.apos;s model describes the experimental observations more accurately than other limiting‐case models that are either too aggressive or too passive in capturing the mixed‐substrate growth rates and intermediate lag periods. Monte Carlo analysis of computational growth experiments in which strains obeying different regulatory policies directly compete for available nutrients reveals that the Matching and Proportional Law policy does not maximize the average growth rate of the culture. However, it allocates metabolic resources more frugally than other policies that outperform it and may be more realistic in reflecting the cellapos;s true fitness‐to‐cost tradeoff as judged by its agreement with experimental growth data.
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
Authors: Hellenthal Garrett , Stephens Matthew 
Published: December 2006

AbstractSummary: We have incorporated both crossover and gene conversion hotspots into an existing coalescent-based program for simulating genetic variation data for a sample of chromosomes from a population.Availability: The source code for msHOT is available at , along with accompanying instructions.Contact: hellenth@stats.ox.ac.uk
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage
Authors: Garzón José Ignacio , Kovacs Julio , Abagyan Ruben , Chacón Pablo 
Published: December 2006

AbstractMotivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning.Results: This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage.Availability: Contact: pablo@cib.csic.esSupplementary information: Supplementary data are available at Bioinformatics online.
Death potentially secondary to sub‐Tenon's block
Authors: Quantock C. L. , Goswami T. 
Published: December 2006

SummaryAn 82‐year‐old ASA 2 patient underwent routine sub‐Tenon's block for cataract surgery. One minute after injection of the local anaesthetic, the patient had a generalised tonic‐clonic seizure and developed refractory ventricular fibrillation; subsequent resuscitation was unsuccessful. With no evidence for intravascular injection, the lack of structural brain abnormalities, and the most striking feature on post mortem examination being severe triple vessel coronary artery disease, it was concluded that this was primarily cardiac in origin; however, the possibility of brainstem anaesthesia should also be considered.
Availability of comparative trials for the assessment of new medicines in the European Union at the moment of market authorization
Authors: Van Luijn Johan C. F. , Gribnau Frank W. J. , Leufkens Hubert G. M. 
Published: December 2006

What is already known about this subject • The assessment of the added therapeutic value of new medicines with a new active substance is hampered by the lack of appropriate comparative information.• Though the extent of this information gap is generally perceived as substantial, it has not been quantified. What this study adds • Information from active controlled trials was available in less than half of the new medicines studied, constituting a significant hurdle for evidence‐based decisionmaking on the use of new medicines in initial years following market introduction.AimsTo investigate the availability of information about premarketing randomized active‐control trials (RaCTs) involving medicines with a new active substance at the moment of market authorization in the European Union.MethodsInformation was obtained from the EMEA European Public Assessment Reports and the MEDLINE and EMBASE databases.ResultsBetween 1999 and 2005, 48% of recently approved medicines (n = 122) had been studied in comparison with existing medicines at the moment of market authorization. About one‐third of these trials were published and publicly available at that moment.ConclusionsFor most new medicines evidence‐based assessment of the (added) therapeutic value is not really possible at the moment of market authorization.
Renal graft survival is not influenced by a positive flow B‐cell crossmatch
Authors: Bryan Christopher F , Wakefield Mark , Reese Jeffrey C , Shield Charles F , Warady Bradley A , Winklhofer Franz T , Murillo Daniel 
Published: December 2006

Abstract: Introduction: The influence of a positive B‐cell crossmatch on graft outcome in renal transplantation is controversial.Methods: We analyzed graft survival using Kaplan–Meier estimates for recipients of deceased donor kidneys who were either regraft transplant patients (n = 198) from 1990 to August 20, 2004, or primary transplant patients (n = 361) from December 15, 2000 to August 8, 2004, each of whom had a flow T‐ and B‐cell IgG crossmatch performed before transplantation. The flow B‐cell crossmatch (FBXM) was not used to decide whether or not to transplant. Graft survival was analyzed by whether the patient's FBXM was positive or negative. We also evaluated creatinine levels and graft survival of 131 transplant patients (June 1, 2004 to July 1, 2005) by their FBXM result and by their HLA class II flow‐defined IgG PRA.Results: One‐ and three‐yr graft survival for the primary transplant patient group with a positive FBXM (98% and 84%) was not significantly different from the group with a negative FBXM (96% and 93%) (log‐rank = 0.9). Similarly, graft survival at one, five, and 10 yr for the regraft transplant group whose FBXM was positive (91%, 76%, and 61%) was not significantly different from the group whose FBXM was negative (91%, 79%, and 77%) (log‐rank = 0.4). Creatinine levels in the group of patients whose FBXM was positive (1.4 ± 0.4 mg/dL; n = 76) were not significantly different from the group with a negative FBXM (1.4 ± 0.4 mg/dL; n = 42). Even in the presence of class II PRA, a positive FBXM did not impact a patient's creatinine levels or graft outcome.Conclusion: Neither short nor long‐term graft survival of deceased donor kidneys is influenced by a positive flow B‐cell IgG crossmatch, even when caused by HLA class II antibody.
Easy Mesh Cutting
Authors: Ji Zhongping , Liu Ligang , Chen Zhonggui , Wang Guojin 
Published: December 2006

Abstract We present Easy Mesh Cutting, an intuitive and easy‐to‐use mesh cutout tool. Users can cut meaningful components from meshes by simply drawing freehand sketches on the mesh. Our system provides instant visual feedback to obtain the cutting results based on an improved region growing algorithm using a feature sensitive metric. The cutting boundary can be automatically optimized or easily edited by users. Extensive experimentation shows that our approach produces good cutting results while requiring little skill or effort from the user and provides a good user experience. Based on the easy mesh cutting framework, we introduce two applications including sketch‐based mesh editing and mesh merging for geometry processing. Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Geometric algorithms, languages, and systems
Accurate Specular Reflections in Real‐Time
Authors: Roger David , Holzschuch Nicolas 
Published: December 2006

Abstract Specular reflections provide many important visual cues in our daily environment. They inform us of the shape of objects, of the material they are made of, of their relative positions, etc. Specular reflections on curved objects are usually approximated using environment maps. In this paper, we present a new algorithm for real‐time computation of specular reflections on curved objects, based on an exact computation for the reflection of each scene vertex. Our method exhibits all the required parallax effects and can handle arbitrary proximity between the reflector and the reflected objects. Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism
Reflected‐Scene Impostors for Realistic Reflections at Interactive Rates
Authors: Popescu Voicu , Mei Chunhui , Dauble Jordan , Sacks Elisha 
Published: December 2006

Abstract We present a technique for rendering reflections on complex reflectors at interactive rates based on approximating the geometry of the reflected scene with impostors. The reflections correctly convey the distance to the reflector surface and provide motion parallax. Two types of impostors are adapted to the reflections framework: billboards and depth maps. Billboards remove most of the problems of environment mapped reflections at only a small additional cost. Second order reflections are supported by introducing reflective billboards. Higher quality reflections that provide motion parallax within a reflected object are obtained by approximating the reflective geometry with depth maps. The computation of the intersection between a reflected ray and a depth map is accelerated by leveraging epipolar constraints. Like environment mapping, our technique does not pose any restriction on the geometry of the reflector, supports dynamic scenes, and runs at interactive rates with the help of graphics hardware. Categories and Subject Descriptors (ACM CCS): I.3.3. [Computer Graphics]—Three‐Dimensional Graphics and Realism.
Multiresolution Random Accessible Mesh Compression
Authors: Kim Junho , Choe Sungyul , Lee Seungyong 
Published: December 2006

Abstract This paper presents a novel approach for mesh compression, which we call multiresolution random accessible mesh compression. In contrast to previous mesh compression techniques, the approach enables us to progressively decompress an arbitrary portion of a mesh without decoding other non‐interesting parts. This simultaneous support of random accessibility and progressiveness is accomplished by adapting selective refinement of a multiresolution mesh to the mesh compression domain. We present a theoretical analysis of our connectivity coding scheme and provide several experimental results. The performance of our coder is about 11 bits for connectivity and 21 bits for geometry with 12‐bit quantization, which can be considered reasonably good under the constraint that no fixed neighborhood information can be used for coding to support decompression in a random order.Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling
C‐BDAM – Compressed Batched Dynamic Adaptive Meshes for Terrain Rendering
Authors: Gobbetti E. , Marton F. , Cignoni P. , Di Benedetto M. , Ganovelli F. 
Published: December 2006

Abstract We describe a compressed multiresolution representation for supporting interactive rendering of very large planar and spherical terrain surfaces. The technique, called Compressed Batched Dynamic Adaptive Meshes (C‐BDAM), is an extension of the BDAM and P‐BDAM chunked level‐of‐detail hierarchy. In the C‐BDAM approach, all patches share the same regular triangulation connectivity and incrementally encode their vertex attributes using a quantized representation of the difference with respect to values predicted from the coarser level. The structure provides a number of benefits: simplicity of data structures, overall geometric continuity for planar and spherical domains, support for variable resolution input data, management of multiple vertex attributes, efficient compression and fast construction times, ability to support maximum‐error metrics, real‐time decompression and shaded rendering with configurable variable level‐of‐detail extraction, and runtime detail synthesis. The efficiency of the approach and the achieved compression rates are demonstrated on a number of test cases, including the interactive visualization of a 29 gigasample reconstruction of the whole planet Earth created from high resolution SRTM data.Categories and Subject Descriptors (according toACMCCS): I.3.3 [Computer Graphics]: Picture and Image Generation; I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism.
Texture Adaptation for Progressive Meshes
Authors: Chen Chih‐Chun , Chuang Jung‐Hong 
Published: December 2006

Abstract Level‐of‐detail modeling is a vital representation for real‐time applications. To support texture mapping progressive meshes (PM), we usually allow the whole PM sequence to share a common texture map. Although such a common texture map can be derived by using appropriate mesh parameterizations that consider the minimization of geometry stretch, texture stretch, or even the texture deviation introduced by edge collapses, we have found that even with a well parameterized texture map, the texture mapped PM still reveals apparent texture distortion due to geometry changes and the nature of linear interpolation used by texture mapping hardware. In this paper, we propose a novel, simple, and efficient approach that adapts texture content for each edge collapse, aiming to eliminate texture distortion. A texture adaptation and its inverse are local and incremental operations that can be fully supported by texture mapping hardware, the render‐to‐texture feature, and the fragment shader. Once the necessary correspondence in the partition of texture space is built during the course of PM construction, the texture adaptation or its inverse can be applied on the fly before rendering the simplified or refined model with texture map. We also propose the mechanism of indexing mapping to reduce blurred artifacts due to under‐sampling that might be introduced by texture adaptation. Keywords: texture mapping progressive meshes, mesh simplification, mesh parameterization, texture distortion Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism Color, shading, shadowing, and texture
Optimizing Control Variate Estimators for Rendering
Authors: Fan Shaohua , Chenney Stephen , Hu Bo , Tsui Kam‐Wah , Lai Yu‐chi 
Published: December 2006

Abstract We present the Optimizing Control Variate (OCV) estimator, a new estimator for Monte Carlo rendering. Based upon a deterministic sampling framework, OCV allows multiple importance sampling functions to be combined in one algorithm. Its optimizing nature addresses a major problem with control variate estimators for rendering: users supply a generic correlated function which is optimized for each estimate, rather than a single highly tuned one that must work well everywhere. We demonstrate OCV with both direct lighting and irradiance‐caching examples, showing improvements in image error of over 35% in some cases, for little extra computation time. Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism Color, shading, shadowing, and texture G.3 [Probability and Statistics]: Probabilistic Algorithms
Keywords:

direct lighting, deterministic mixture sampling, control variates
A Predictive Light Transport Model for the Human Iris
Authors: W.Y. Lam Michael , V.G. Baranoski Gladimir 
Published: December 2006

Abstract Recently, light interactions with organic matter have become the object of detailed investigations by image synthesis researchers. Besides allowing these materials to be rendered in a more intuitive manner, these efforts aim to extend the scope of computer graphics applications to areas such as applied optics and biomedical imaging. There are, however, organic materials that still lack predictive simulation solutions. Among these, the ocular tissues, especially those forming the human iris, pose the most challenging modeling problems which are often associated with data scarcity. In this paper, we describe the first biophysically‐based light transport model for the human iris ever presented in the scientific literature. The proposed model algorithmically simulates the light scattering and absorption processes occurring within the iridal tissues, and computes the spectral radiometric responses of these tissues. Its design is based on the current scientific understanding of the iridal morphological and optical characteristics, and it is controlled by parameters directly related to these biophysical attributes. The accuracy and predictability of the spectral results provided by the model are evaluated through comparisons with actual measured iridal data, and its integration into rendering frameworks is illustrated through the generation of images depicting iridal chromatic variations. Categories and Subject Descriptors (according to ACM CCS): I.3.8 [Computer Graphics]: Applications
Bayesian Point Cloud Reconstruction
Authors: Jenke P. , Wand M. , Bokeloh M. , Schilling A. , Straßer W. 
Published: December 2006

Abstract In this paper, we propose a novel surface reconstruction technique based on Bayesian statistics: The measurement process as well as prior assumptions on the measured objects are modeled as probability distributions and Bayes’ rule is used to infer a reconstruction of maximum probability. The key idea of this paper is to define both measurements and reconstructions as point clouds and describe all statistical assumptions in terms of this finite dimensional representation. This yields a discretization of the problem that can be solved using numerical optimization techniques. The resulting algorithm reconstructs both topology and geometry in form of a well‐sampled point cloud with noise removed. In a final step, this representation is then converted into a triangle mesh. The proposed approach is conceptually simple and easy to extend. We apply the approach to reconstruct piecewise‐smooth surfaces with sharp features and examine the performance of the algorithm on different synthetic and real‐world data sets. Categories and Subject Descriptors (according to ACM CCS): I.5.1 [Models]: Statistical; I.3.5 [Computer Graphics]: Curve, surface, solid and object representations
Competing Fronts for Coarse–to–Fine Surface Reconstruction
Authors: Sharf Andrei , Lewiner Thomas , Shamir Ariel , Kobbelt Leif , Cohen–Or Daniel 
Published: December 2006

Abstract We present a deformable model to reconstruct a surface from a point cloud. The model is based on an explicit mesh representation composed of multiple competing evolving fronts. These fronts adapt to the local feature size of the target shape in a coarse–to–fine manner. Hence, they approach towards the finer (local) features of the target shape only after the reconstruction of the coarse (global) features has been completed. This conservative approach leads to a better control and interpretation of the reconstructed topology. The use of an explicit representation for the deformable model guarantees water‐tightness and simple tracking of topological events. Furthermore, the coarse–to–fine nature of reconstruction enables adaptive handling of non‐homogenous sample density, including robustness to missing data in defected areas.Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: Digitizing and scanning. Keywords: surface reconstruction, deformable models
Analysis of Reproducing Real‐World Appearance on Displays of Varying Dynamic Range
Authors: Yoshida Akiko , Mantiuk Rafał , Myszkowski Karol , Seidel Hans‐Peter 
Published: December 2006

Abstract We conduct a series of experiments to investigate the desired properties of a tone mapping operator (TMO) and to design such an operator based on subjective data. We propose a novel approach to the tone mapping problem, in which the tone mapping parameters are determined based on the data from subjective experiments, rather than an image processing algorithm or a visual model. To collect this data, a series of experiments are conducted in which the subjects adjust three generic TMO parameters: brightness, contrast and color saturation. In two experiments, the subjects are to find a) the most preferred image without a reference image (preference task) and b) the closest image to the real‐world scene which the subjects are confronted with (fidelity task). We analyze subjects’ choice of parameters to provide more intuitive control over the parameters of a tone mapping operator. Unlike most of the researched TMOs that focus on rendering for standard low dynamic range monitors, we consider a broad range of potential displays, each offering different dynamic range and brightness. We simulate capabilities of such displays on a high dynamic range (HDR) display. This allows us to address the question of how tone mapping needs to be adjusted to accommodate displays with drastically different dynamic ranges.Categories and Subject Descriptors (according to ACM CCS): I.3.8 [Computer Graphics]: High dynamic range images, Visual perception, Tone mapping
GPU‐based Collision Detection for Deformable Parameterized Surfaces
Authors: Greß Alexander , Guthe Michael , Klein Reinhard 
Published: December 2006

Abstract Based on the potential of current programmable GPUs, recently several approaches were developed that use the GPU to calculate deformations of surfaces like the folding of cloth or to convert higher level geometry to renderable primitives like NURBS or subdivision surfaces. These algorithms are realized as a per‐frame operation and take advantage of the parallel processing power of the GPU. Unfortunately, an efficient accurate collision detection, that is necessary for the simulation itself or for the interaction with and editing of the objects, can currently not be integrated seamlessly into these GPU‐based approaches without switching back to the CPU. In this paper we describe a novel GPU‐based collision detection method for deformable parameterized surfaces that can easily be combined with the aforementioned approaches. Representing the individual parameterized surfaces by stenciled geometry images allows to generate GPU‐optimized bounding volume hierarchies in real‐time that serve as a basis for an optimized GPU‐based hierarchical collision detection algorithm. As a test case we applied our algorithm to the collision detection of deformable trimmed NURBS models, which is an important problem in industry. For the trimming and tessellation of the NURBS on the GPU we used a recent approach [GBK05] and combined it with our collision detection algorithm. This way we are able to render and check collisions for deformable models consisting of several thousands of trimmed NURBS patches in real‐time. Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling—Geometric algorithms, languages, and systems; Splines; I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism—Virtual reality