bluuebunny/crossref_metadata_2025 huggingface dataset:
σ B-dependent expression patterns of compatible solute transporter genes opuCA and lmo1421 and the conjugated bile salt hydrolase gene bsh in Listeria monocytogenes
Authors: Sue David , Boor Kathryn J. , Wiedmann Martin
Published: November 2003

Listeria monocytogenesis a food-borne pathogen that can persist and grow under a wide variety of environmental conditions including low pH and high osmolarity. The alternative sigma factorσBcontributes toL. monocytogenessurvival under extreme conditions. The purpose of this study was to identify and confirm specificσB-dependent genes inL. monocytogenesand to characterize their expression patterns under various stress conditions.opuCA,lmo1421andbshwere identified as putativeσB-dependent genes based on the presence of a predictedσB-dependent promoter sequence upstream of each gene.opuCAandlmo1421encode known and putative compatible solute transporter proteins, respectively, andbshencodes a conjugated bile salt hydrolase (BSH). Reporter fusions and semi-quantitative RT-PCR techniques were used to confirmσB-dependent regulation of these stress-response genes and to determine their expression patterns in response to environmental stresses. RT-PCR demonstrated thatopuCA,lmo1421andbshtranscript levels are reduced in stationary-phaseL. monocytogenesΔsigBcells relative to levels present in wild-type cells. Furthermore, BSH activity is abolished in aL. monocytogenesΔsigBstrain. RT-PCR confirmed growth-phase-dependent expression ofopuCA, with highest levels of expression in stationary-phase cells. TheL. monocytogeneswild-type strain exhibited two- and threefold induction ofopuCAexpression and seven- and fivefold induction oflmo1421expression following 10 and 15 min exposure to 0·5 M KCl, respectively, as determined by RT-PCR, suggesting rapid induction ofσBactivity in exponential-phaseL. monocytogenesupon exposure to salt stress. Single-copy chromosomalopuCA–gusreporter fusions also showed significant induction ofopuCAexpression following exposure of exponential-phase cells to increased salt concentrations (0·5 M NaCl or 0·5 M KCl). In conjunction with recent findings that indicate a role foropuCAandbshinL. monocytogenesvirulence, the data presented here provide further evidence of specificσB-mediated contributions to both environmental stress resistance and intra-host survival inL. monocytogenes.
Characterization of the LlaCI methyltransferase from Lactococcus lactis subsp. cremoris W15 provides new insights into the biology of type II restriction–modification systems
Authors: Mruk Iwona , Cichowicz Magdalena , Kaczorowski Tadeusz
Published: November 2003

The gene encoding the LlaCI methyltransferase (M.LlaCI) fromLactococcus lactissubsp.cremorisW15 was overexpressed inEscherichia coli. The enzyme was purified to apparent homogeneity using three consecutive steps of chromatography on phosphocellulose, blue-agarose and Superose 12HR, yielding a protein ofMr31 300±1000 under denaturing conditions. The exact position of the start codon AUG was determined by protein microsequencing. This enzyme recognizes the specific palindromic sequence 5′-AAGCTT-3′. Purified M.LlaCI was characterized. Unlike many other methyltransferases, M.LlaCI exists in solution predominantly as a dimer. It modifies the first adenine residue at the 5′ end of the specific sequence toN6-methyladenine and thus is functionally identical to the corresponding methyltransferases of the HindIII (Haemophilus influenzaeRd) and EcoVIII (Escherichia coliE1585-68) restriction–modification systems. This is reflected in the identity of M.LlaCI with M.HindIII and M.EcoVIII noted at the amino acid sequence level (50 % and 62 %, respectively) and in the presence of nine sequence motifs conserved amongN6-adenineβ-class methyltransferases. However, polyclonal antibodies raised against M.EcoVIII cross-reacted with M.LlaCI but not with M.HindIII. Restriction endonucleases require Mg2+for phosphodiester bond cleavage. Mg2+was shown to be a strong inhibitor of the M.LlaCI enzyme and its isospecific homologues. This observation suggests that sensitivity of the M.LlaCI to Mg2+may strengthen the restriction activity of the cognate endonuclease in the bacterial cell. Other biological implications of this finding are also discussed.
Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network
Authors: Zak Daniel E. , Gonye Gregory E. , Schwaber James S. , Doyle Francis J.
Published: November 2003

Gene expression profiles are an increasingly common data source that can yield insights into the functions of cells at a system-wide level. The present work considers the limitations in information content of gene expression data for reverse engineering regulatory networks. An in silico genetic regulatory network was constructed for this purpose. Using the in silico network, a formal identifiability analysis was performed that considered the accuracy with which the parameters in the network could be estimated using gene expression data and prior structural knowledge (which transcription factors regulate which genes) as a function of the input perturbation and stochastic gene expression. The analysis yielded experimentally relevant results. It was observed that, in addition to prior structural knowledge, prior knowledge of kinetic parameters, particularly mRNA degradation rate constants, was necessary for the network to be identifiable. Also, with the exception of cases where the noise due to stochastic gene expression was high, complex perturbations were more favorable for identifying the network than simple ones. Although the results may be specific to the network considered, the present study provides a framework for posing similar questions in other systems.
Limitations of Quantitative Gene Regulation Models: A Case Study
Authors: Kim Philip M. , Tidor Bruce
Published: November 2003

Understanding the relationship between network structure and behavior is fundamental to the field of computational and systems biology. A particularly important distinction is the extent to which qualitative aspects of network performance are encoded in network topology as opposed to being determined through quantitative details, such as those of kinetics. Here, we develop a general and rigorous mathematical framework for the analysis of genetic networks and apply it to a family of synthetic gene networks. A key feature of our methodology involves determining network behavior that is insensitive to kinetic parameters such as rate constants and nonlinear functional dependencies of rates on molecular concentrations. Results indicate that behavior observed in some networks cannot be reconciled with standard gene expression and regulation models. We explore relaxing model assumptions to explain the observed behavior, allowing for both dynamicand stochastic phenomena, and propose an alternative model. Our alternative model includes the suggestion of a new mechanism by which the counterintuitive behavior could be achieved; central to the model is the assumption that the Clp protein degradation system, which is responsible for the regulatory proteins used in this study, becomes saturated.
Toward Rigorous Comprehension of Biological Complexity: Modeling, Execution, and Visualization of Thymic T-Cell Maturation
Authors: Efroni Sol , Harel David , Cohen Irun R.
Published: November 2003

One of the problems biologists face is a data set too large to comprehend in full. Experimenters generate data at an ever-growing pace, each from their own niche of interest. Current theories are each able, at best, to capture and model only a small part of the data. We aim to develop a general approach to modeling that will help broaden biological understanding. T-cell maturation in the thymus is a telling example of the accumulation of experimental data into a large disconnected data set. The thymus is responsible for the maturation of stem cells into mature T cells, and its complexity divides research into different fields, for example, cell migration, cell differentiation, histology, electron microscopy, biochemistry, molecular biology, and more. Each field forms its own viewpoint and its own set of data. In this study we present the results of a comprehensive integration of large parts of this data set. The integration is performed in a two-tiered visual manner. First, we use the visual language of Statecharts, which makes specification precise, legible, and executable on computers. We then set up a moving graphical interface that dynamically animates the cells, their receptors, the different gradients, and the interactions that constitute thymic maturation. This interface also provides a means for interacting with the simulation.
A Biophysical Approach to Transcription Factor Binding Site Discovery
Authors: Djordjevic Marko , Sengupta Anirvan M. , Shraiman Boris I.
Published: November 2003

Identification of transcription factor binding sites within regulatory segments of genomic DNA is an important step toward understanding of the regulatory circuits that control expression of genes. Here, we describe a novel bioinformatics method that bases classification of potential binding sites explicitly on the estimate of sequence-specific binding energy of a given transcription factor. The method also estimates the chemical potential of the factor that defines the threshold of binding. In contrast with the widely used information-theoretic weight matrix method, the new approach correctly describes saturation in the transcription factor/DNA binding probability. This results in a significant improvement in the number of expected false positives, particularly in the ubiquitous case of low-specificity factors. In the strong binding limit, the algorithm is related to the “support vector machine” approach to pattern recognition. The new method is used to identify likely genomic binding sites for the E. coli transcription factors collected in the DPInteract database. In addition, for CRP (a global regulatory factor), the likely regulatory modality (i.e., repressor or activator) of predicted binding sites is determined.
Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles
Authors: Gutiérrez-Ríos Rosa María , Rosenblueth David A. , Loza José Antonio , Huerta Araceli M. , Glasner Jeremy D. , Blattner Fred R. , Collado-Vides Julio
Published: November 2003

The transcriptional network of Escherichia coli may well be the most complete experimentally characterized network of a single cell. A rule-based approach was built to assess the degree of consistency between whole-genome microarray experiments in different experimental conditions and the accumulated knowledge in the literature compiled in RegulonDB, a data base of transcriptional regulation and operon organization in E. coli. We observed a high and statistical significant level of consistency, ranging from 70%-87%. When effector metabolites of regulatory proteins are not considered in the prediction of the active or inactive state of the regulators, consistency falls by up to 40%. Similarly, consistency decreases when rules for multiple regulatory interactions are altered or when “on” and “off” entries were assigned randomly. We modified the initial state of regulators and evaluated the propagation of errors in the network that do not correlate linearly with the connectivity of regulators. We interpret this deviation mainly as a result of the existence of redundant regulatory interactions. Consistency evaluation opens a new space of dialogue between theory and experiment, as the consequences of different assumptions can be evaluated and compared.
Staff attitudes to the development and delivery of e‐learning
Authors: Newton Robert
Published: November 2003

Reports the outcome of research conducted as part of a project funded by the Learning and Technology Support Network – Information and Computing Studies Group (LTSN‐ICS). The paper deals with the issues perceived as being important “barriers” to using technology in teaching and learning within the academic staff community working in higher education in the UK. Data were gathered from a critical analysis of the literature, the administration of a questionnaire survey and a series of interviews with academic staff. Empirical data are used to verify some of the contentions from the literature review and to contextualise these (mainly US‐based publications) in terms of the experience of UK academics. The overall picture which emerges when examining a range of initiatives currently being undertaken across a range of academic institutions is that developments are often led by the enthusiasm of individuals with little extrinsic reward structure to encourage these innovations.
A self‐help approach to knowledge management benchmarking
Authors: Carpenter Simon , Rudge Sarah
Published: November 2003

This paper discusses a knowledge management (KM) benchmarking exercise conducted at British Energy Power and Trading (BEPET). Current knowledge management activities were benchmarked against key areas in the British Standard Guide to Good Practice in Knowledge Management, PAS 2001. The knowledge performance categories identified by the international knowledge management Most Admired Knowledge Enterprises (MAKE) awards for 2001 were used as a basis for a staff survey to determine KM activity within the division. A knowledge audit of BEPET staff was also carried out to gain greater insight of the knowledge flows within the organization. In addition to the study’s findings, the paper discusses the concepts of benchmarking, organizational culture and knowledge audits, providing a context for their application in KM.
Open Issues in Photo‐realistic Rendering
Authors: Purgathofer Werner
Published: November 2003

For more than two decades Computer graphics researchers have tried to achieve photo‐realism in their images as reliable as possible, mainly by simulating the physical laws of light and adding one effect after the other. The recent years have brought a change of efforts towards real‐time methods, easy‐to‐use systems, integration with vision, modelling tools and the like. The quality of images is mostly accepted as sufficient for real world applications, but where are we really? There are still numerous problems to be solved, and there is notable progress in these areas. No question, the plug‐in philosophy of some commercial products has enabled several of these new techniques to be distributed quite fast. But unfortunately, many other of these developments happen in isolated systems for the pure purpose of publication, and never make it into commercial software. This presentation wants to make people more aware of such activities, and evaluate the steps we still have to go towards perfect photo‐realism.

The talk will start with an attempt to give a brief overview of the rendering history, highlighting the main research directions at different times. It will explain the driving forces of the developments, which are complexity, speed, and accuracy, and maybe also expression in recent years. Solved and unsolved areas are examined, and compared to practically solved but theoretically incomplete topics such as translucency, tone mapping, light source and BTF descriptions, and error metrics for image quality evaluation. The difference lies mainly in the difference between believable, correct, and predictive images. Also, for really realistic images modelling complexity is still an issue. Finally, some recent work on polarization and fluorescence is presented.
Animation of Bubbles in Liquid
Authors: Hong Jeong‐Mo , Kim Chang‐Hun
Published: November 2003

We present a new fluid animation technique in which liquid and gas interact with each other, using the exampleof bubbles rising in water. In contrast to previous studies which only focused on one fluid, our system considersboth the liquid and the gas simultaneously. In addition to the flowing motion, the interactions between liquid andgas cause buoyancy, surface tension, deformation and movement of the bubbles. For the natural manipulationof topological changes and the removal of the numerical diffusion, we combine the volume‐of‐fluid method andthe front‐tracking method developed in the field of computational fluid dynamics. Our minimum‐stress surfacetension method enables this complementary combination. The interfaces are constructed using the marching cubesalgorithm. Optical effects are rendered using vertex shader techniques.

Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Animation
Cloth Motion Capture
Authors: Pritchard D. , Heidrich W.
Published: November 2003

Recent years have seen an increased interest in motion capture systems. Current systems, however, are limitedto only a few degrees of freedom, so that effectively only the motion of linked rigid bodies can be acquired. Wepresent a system for the capture of deformable surfaces, most notably moving cloth, including both geometry andparameterisation. We recover geometry using stereo correspondence, and use the Scale Invariant Feature Transform(SIFT) to identify an arbitrary pattern printed on the cloth, even in the presence of fast motion. We describea novel seed‐and‐grow approach to adapt the SIFT algorithm to deformable geometry. Finally, we interpolatefeature points to parameterise the complete geometry.

Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Physically based modelingI.4.8 [Image Processing and Computer Vision]: Scene analysis
Compression of 2D Vector Fields Under Guaranteed Topology Preservation
Authors: Theisel H. , Rössl Ch. , Seidel H.‐P.
Published: November 2003

In this paper we introduce a new compression technique for 2D vector fields which preserves the complete topology, i.e., the critical points and the connectivity of the separatrices. As the theoretical foundation of the algorithm, we show in a theorem that for local modifications of a vector field, it is possible to decide entirely by a local analysis whether or not the global topology is preserved. This result is applied in a compression algorithm which is based on a repeated local modification of the vector field ‐ namely a repeated edge collapse of the underlying piecewise linear domain. We apply the compression technique to a number of data sets with a complex topology and obtain significantly improved compression ratios in comparison to pre‐existing topology‐preserving techniques.
Out‐of‐core compression and decompression of large n‐dimensional scalar fields
Authors: Ibarria Lawrence , Lindstrom Peter , Rossignac Jarek , Szymczak Andrzej
Published: November 2003

We present a simple method for compressing very large and regularly sampled scalar fields. Our method is particularlyattractive when the entire data set does not fit in memory and when the sampling rate is high relative to thefeature size of the scalar field in all dimensions. Although we report results for

and

data sets, the proposedapproach may be applied to higher dimensions. The method is based on the new Lorenzo predictor, introducedhere, which estimates the value of the scalar field at each sample from the values at processed neighbors. The predictedvalues are exact when the n‐dimensional scalar field is an implicit polynomial of degree

n− 1. Surprisingly,when the residuals (differences between the actual and predicted values) are encoded using arithmetic coding,the proposed method often outperforms wavelet compression in anL∞sense. The proposed approach may beused both for lossy and lossless compression and is well suited for out‐of‐core compression and decompression,because a trivial implementation, which sweeps through the data set reading it once, requires maintaining only asmall buffer in core memory, whose size barely exceeds a single (n−1)‐dimensional slice of the data.

Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Compression, scalar fields,out‐of‐core.
Precise Ink Drawing of 3D Models
Authors: Sousa Mario Costa , Foster Kevin , Wyvill Brian , Samavati Faramarz
Published: November 2003

Drawings made with precise pen strokes accurately reveal the geometric forms that give subjects their characteristicshape. We present a system for non‐photorealistic rendering of precise drawing strokes over dense 3Dtriangle meshes with arbitrary topology. During an automatic pre‐process, we construct an extended version ofthe edge‐buffer data structure to allow the calculation of shape measures at each mesh edge, by adapting numericalmethods used in geomorphology. At runtime, feature edges related to shape measures are extracted andrendered as strokes with varying thickness and pen marking styles. Stroke thickness is automatically adjusted byconsidering surface curvature. Pen marking styles and visual effects of ink distribution are both controlled by theuser. We demonstrate precise drawing strokes over complex meshes revealing a variety of shape characteristics.
Multiresolution Surface Representation Based on Displacement Volumes
Authors: Botsch Mario , Kobbelt Leif
Published: November 2003

We propose a new representation for multiresolution models which uses volume elements enclosed between thedifferent resolution levels to encode the detail information. Keeping these displacement volumes locally constantduring a deformation of the base surface leads to a natural behaviour of the detail features. The correspondingreconstruction operator can be implemented efficiently by a hierarchical iterative relaxation scheme, providingclose to interactive response times for moderately complex models.

Based on this representation we implement a multiresolution editing tool for irregular polygon meshes that allowsthe designer to freely edit the base surface of a multiresolution model without having to care about self‐intersectionsin the respective detailed surface. We demonstrate the effectiveness and robustness of the reconstructionby several examples with real‐world data.
Progressive Simplification of Tetrahedral Meshes Preserving All Isosurface Topologies
Authors: Chiang Yi‐Jen , Lu Xiang
Published: November 2003

In this paper, we propose a novel technique for constructing multiple levels of a tetrahedral volume dataset whilepreserving the topologies of all isosurfaces embedded in the data. Our simplification technique has two majorphases. In the segmentation phase, we segment the volume data into topological‐equivalence regions, that is, thesub‐volumes within each of which all isosurfaces have the same topology. In the simplification phase, we simplifyeach topological‐equivalence region independently, one by one, by collapsing edges from the smallest to the largesterrors (within the user‐specified error tolerance, for a given error metrics), and ensure that we do not collapseedges that may cause an isosurface‐topology change. We also avoid creating a tetrahedral cell of negative volume(i.e., avoid the fold‐over problem). In this way, we guarantee to preserve all isosurface topologies in the entiresimplification process, with a controlled geometric error bound. Our method also involves several additionalnovel ideas, including using the Morse theory and the implicit fully augmented contour tree, identifying typesof edges that are not allowed to be collapsed, and developing efficient techniques to avoid many unnecessary orexpensive checkings, all in an integrated manner. The experiments show that all the resulting isosurfaces preservethe topologies, and have good accuracies in their geometric shapes. Moreover, we obtain nice data‐reductionrates, with competitively fast running times.
BDAM — Batched Dynamic Adaptive Meshes for High Performance Terrain Visualization
Authors: Cignoni P. , Ganovelli F. , Gobbetti E. , Marton F. , Ponchio F. , Scopigno R.
Published: November 2003

This paper describes an efficient technique for out‐of‐core rendering and management of large textured terrainsurfaces. The technique, called Batched Dynamic Adaptive Meshes (BDAM), is based on a paired tree structure:a tiled quadtree for texture data and a pair of bintrees of small triangular patches for the geometry. These smallpatches are TINs and are constructed and optimized off‐line with high quality simplification and tristrippingalgorithms. Hierarchical view frustum culling and view‐dependent texture and geometry refinement is performedat each frame through a stateless traversal algorithm. Thanks to the batched CPU/GPU communication model,the proposed technique is not processor intensive and fully harnesses the power of current graphics hardware.Both preprocessing and rendering exploit out‐of‐core techniques to be fully scalable and to manage large terraindatasets.

Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: Picture and Image Generation;I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism.
Beyond Stippling  — Methods for Distributing Objects on the Plane
Authors: Hiller Stefan , Hellwig Heino , Deussen Oliver
Published: November 2003

Conventionally, stippling is an effective technique for representing surfaces in pen‐and‐ink. We present new efficientmethods for stipple drawings by computer. In contrast to already existing techniques, arbitrary shapes canbe used in place of dots. An extension of Lloyd's Method enables us to position small objects on a plane in a visuallypleasing form. This allows us to generate new illustration styles. Similar methods can be used for positioningobjects in other applications.
Reanimating Faces in Images and Video
Authors: Blanz V. , Basso C. , Poggio T. , Vetter T.
Published: November 2003

This paper presents a method for photo‐realistic animation that can be applied to any face shown in a single imageor a video. The technique does not require example data of the person's mouth movements, and the image to beanimated is not restricted in pose or illumination. Video reanimation allows for head rotations and speech in theoriginal sequence, but neither of these motions is required.

In order to animate novel faces, the system transfers mouth movements and expressions across individuals, basedon a common representation of different faces and facial expressions in a vector space of 3D shapes and textures.This space is computed from 3D scans of neutral faces, and scans of facial expressions.

The 3D model's versatility with respect to pose and illumination is conveyed to photo‐realistic image and videoprocessing by a framework of analysis and synthesis algorithms: The system automatically estimates 3D shape andall relevant rendering parameters, such as pose, from single images. In video, head pose and mouth movements aretracked automatically. Reanimated with new mouth movements, the 3D face is rendered into the original images.

Categories and Subject Descriptors (according to ACM CCS): I.3.7 [Computer Graphics]: Animation
Advanced Design for a Realistic Virtual Brush
Authors: Xu Songhua , Lau Francis C.M. , Tang Feng , Pan Yunhe
Published: November 2003

This paper proposes a novel algorithmic framework for an advanced virtual brush to be used in interactive digitalpainting. The framework comprises the following components: a geometry model of the brush using a hierarchicalrepresentation that leads to substantial savings in every step of the painting process; fast online brush motionsimulation assisted by offline calibration that guarantees an accurate and stable simulation of the brush's dynamicbehavior; a new pigment model based on a diffusion process of random molecules that considers delicateand complex pigment behavior at dipping time as well as during painting; and a user‐adaptation component thatenables the system to cater for the personal painting habits of different users. A prototype system has been implementedbased on this framework. Compared with other virtual brushes, this new system is designed to presenta realistic brush in the sense that the system accurately and stably simulates the complex painting functionalityof a running brush, and therefore is capable of creating high‐quality digital paintings with minute aesthetic detailsthat can rival the real artwork. The advanced features also give rise to a high degree of expressiveness ofthe virtual brush that the user can comfortably manipulate. http://www.csis.hku.hk/songhuale‐brush/ providessupplementary materials for this paper.

Categories and Subject Descriptors (according to ACM CCS): I.3.6 [Methodology and Techniques]: Interactiontechniques; I.3.5 [Computational Geometry and Object Modeling]: Physically based modeling; I.3.4 [GraphicsUtilities]: Paint systems;
Control of human mandibular posture during locomotion
Authors: Miles Timothy S. , Flavel Stanley C. , Nordstrom Michael A.
Published: November 2003

Mandibular movements and masseter muscle activity were measured in humans during hopping, walking and running to determine whether reflexes contribute to the maintenance of jaw position during locomotion. In initial experiments, subjects hopped so that they landed either on their toes or on their heel. Landing on the toes provoked only small mandibular movements and no reflex responses in the masseter electromyogram (EMG). Landing on the heels with the jaw muscles relaxed caused the mandible to move vertically downwards relative to the maxilla, and evoked a brisk reflex response in the masseter at monosynaptic latency. Neither this relative movement of the mandible nor the reflex was seen when the teeth were clenched: hence the reflex is not the result of vestibular activation during head movement. The same variables were measured in a second series of experiments while subjects stood, walked and ran at various speeds and at various inclinations on a treadmill. During walking, the vertical movements of the head and therefore the mandible were slow and small, and there was no tonic masseter EMG or gait‐related activity in the jaw‐closing muscles. When subjects ran, the vertical head and jaw movement depended on the running speed and the inclination of the treadmill. Landing on the heels induced larger movements than landing on the toes. About 10 ms after each foot‐strike, the mandible moved downwards relative to the maxilla, thereby stretching the jaw‐closing muscles and activating them at segmental reflex latency. This caused the mandible to move back upwards. The strength of the reflex response was related to the speed and amplitude of the vertical jaw movement following landing. It is concluded that, during walking, the small, slow movements of the mandible relative to the maxilla are subthreshold for stretch reflexes in the jaw muscles: i.e. the mandible is supported by visco‐elasticity of the soft tissues in the masticatory system. However, the brisker downward movements of the mandible after heel‐landing during hopping and running evoke segmental reflex responses which contribute to the active maintenance of the posture of the mandible. This is a unique demonstration of how a stretch reflex operates to maintain posture under entirely natural conditions.
Mechanosensitive duodenal afferents contribute to vagal modulation of inflammation in the rat
Authors: Miao Frederick Jia‐Pei , Green Paul G. , Levine Jon D.
Published: November 2003

Noxious stimuli inhibit inflammation by activating neuroendocrine stress axes, an effect that is potently attenuated by ongoing activity in subdiaphragmatic vagal afferents. Because this vagal afferent activity is carried in the coeliac and coeliac accessory branches of the subdiaphragmatic vagus, we tested the hypothesis that the activity arises from vagal afferents that innervate a proximal segment of the gastrointestinal tract. Surgical removal of the duodenum, but not the stomach, produces a marked (six orders of magnitude) leftward shift in the dose–response curve for intraplantar capsaicin‐induced inhibition of synovial plasma extravasation induced by the potent inflammatory mediator bradykinin, in the knee joint; this is similar in magnitude to the inhibition produced by subdiaphragmatic or by coeliac plus coeliac accessory branch vagotomy. Fasting, to unload mechanically sensitive polymodal afferents in the proximal gastrointestinal tract, produces a similar leftward shift in the dose–response curve for the inhibitory effect of capsaicin, an effect that is reversed by balloon distension in the duodenum in fasted rats, while balloon distension postvagotomy had no effect. These results suggest that activation of mechanically sensitive vagal afferents in the duodenum contributes vagal afferent activity that modulates neuroendocrine control of the inflammatory response.
Unidimensional models of acoustic propagation in axisymmetric waveguides
Authors: Hélie Thomas
Published: November 2003

This paper presents a model of the linear acoustic propagation in axisymmetric waveguides, the pressure depending on a single space variable. The approach consists of writing the wave equation and the boundary conditions for a coordinate system rectifying the isobaric map at each time. The two-dimensional dependence of the problem is thus transferred from the pressure to the coefficients of the wave equation. From this result, an exclusively geometrical necessary condition is deduced for the admissibility of isobaric maps. However, the knowledge of the waveguide geometry is not sufficient to separate the pressure and the isobaric map solutions. In order to develop a unidimensional wave equation, a geometrical hypothesis is discussed. For lossless and motionless rigid waveguides, the deduced equation leads to exact results for tubes and cones. It may be interpreted as a Webster equation for a particular coordinate system so that the particular profiles for which analytical solutions of the pressure exist are redefined. The wave equation is also established for pipes with visco-thermal losses and, more generally, for mobile walls having a small admittance. The compatibility of the geometrical hypothesis with the exact model is specified for this general case.
Changes in volume reverberation from deep to shallow water in the eastern Gulf of Mexico
Authors: Love Richard H. , Thompson Charles H. , Nero Redwood W.
Published: November 2003

Scattering from fish is a primary cause of volume reverberation and, since fish populations change from deep to shallow water, the character of volume reverberation should also change. However, there are few data available to document expected changes. Therefore, an experiment was conducted in the eastern Gulf of Mexico to investigate possible changes in volume reverberation from deep to slope to shelf waters. Results showed that volume reverberation in outer shelf waters varied more rapidly with respect to both time and space than that in deeper waters. Day-time scattering was similar for deep, slope and shelf waters, total scattering strengths generally increased with frequency. Night-time scattering for the deep ocean and slope also increased with increasing frequency. Scattering modeling suggests that swimbladder-bearing fishes smaller than 10 cm were responsible for the observed volume reverberation. Night-time scattering at the outer shelf location was very different, with strong scattering peaks at low frequencies. Scattering modeling implicates 12–15 cm rough scad and round herring as potential causes of the low frequency peaks. Hence, experiment results confirmed that, as expected, volume reverberation over shelf waters is different and more variable than in deeper waters of the eastern Gulf of Mexico.
Shaping function models of the phonatory excitation signal
Authors: Schoentgen Jean
Published: November 2003

The phonatory excitation signal is the acoustic signal that is generated at the glottis by the vibrating vocal folds and pulsatile airflow. A shaping function model is a nonlinear memoryless input–output characteristic that transforms a simple harmonic into the desired output. The model can be fitted linearly to observed or simulated template cycles. The instantaneous values of the excitation cycle centroid, amplitude as well as length, and the cues for phonatory identity are set via distinct parameters. The synthetic phonatory excitation signal is zero on average, as well as identically zero when the glottal airflow rate is constant.
Locally conformal method for acoustic finite-difference time-domain modeling of rigid surfaces
Authors: Tolan Julius G. , Schneider John B.
Published: November 2003

The finite-difference time-domain method is a simple but powerful numerical method for simulating full-wave acoustic propagation and scattering. However, the method can demand a large amount of computational resources. Traditionally, continuously curved boundaries are represented in a stair-step fashion and thus accurately modeling scattering from a boundary will require a finer discretization than would otherwise be necessary for modeling propagation in a homogeneous medium. However, a fine discretization might not be practical due to limited computational resources. A locally conformal technique is presented here for modeling acoustic scattering from continuously curved rigid boundaries. This technique is low cost, simple to implement, and gives better results for the same grid discretization than the traditional stair-step representation. These improvements can be traded for a coarser discretization which reduces the computational burden. The improved accuracy of this technique is demonstrated for a spherical scatterer.
Spatial unmasking of nearby pure-tone targets in a simulated anechoic environment
Authors: Kopčo Norbert , Shinn-Cunningham Barbara G.
Published: November 2003

Detection thresholds were measured for different spatial configurations of 500- and 1000-Hz pure-tone targets and broadband maskers. Sources were simulated using individually measured head-related transfer functions (HRTFs) for source positions varying in both azimuth and distance. For the spatial configurations tested, thresholds ranged over 50 dB, primarily as a result of large changes in the target-to-masker ratio (TMR) with changes in target and masker locations. Intersubject differences in both HRTFs and in binaural sensitivity were large; however, the overall pattern of results was similar across subjects. As expected, detection thresholds were generally smaller when the target and masker were separated in azimuth than when they were at the same location. However, in some cases, azimuthal separation of target and masker yielded little change or even a small increase in detection threshold. Significant intersubject differences occurred as a result both of differences in monaural and binaural acoustic cues in the individualized HRTFs and of different binaural contributions to performance. Model predictions captured general trends in the pattern of spatial unmasking. However, subject-specific model predictions did not account for the observed individual differences in performance, even after taking into account individual differences in HRTF measurements and overall binaural sensitivity. These results suggest that individuals differ not only in their overall sensitivity to binaural cues, but also in how their binaural sensitivity varies with the spatial position of (and interaural differences in) the masker.
Detection of object resonances by vibro-acoustography and numerical vibrational mode identification
Authors: Mitri Farid G. , Trompette Philippe , Chapelon Jean-Yves
Published: November 2003

Chalk sphere and cylinder resonance frequencies related to compressional and bending modes were detected in water, using vibro-acoustography, a relatively new imaging technique. The variable (radiation) force of low-frequency excitation, produced by intersecting two primary focused ultrasound waves with slightly different frequencies, forces the object to vibrate. The low-frequency acoustic emission field, resulting from object vibration, was detected by a hydrophone. By fixing the object at the focus of the ultrasound beam and sweeping the frequency of one of the primary beams within a chosen bandwidth, it was possible to detect some of the resonance frequencies (those related to compressional and bending modes) via variations in acoustic emission amplitude. Experimental results showed excellent agreement with finite element calculations. This method can be used to characterize the presence of heterogeneities in various media, in the field of materials science or biology.
Effects of reverberation on perceptual segregation of competing voices
Authors: Culling John F. , Hodder Kathryn I. , Toh Chaz Yee
Published: November 2003

Two experiments investigated the effect of reverberation on listeners’ ability to perceptually segregate two competing voices. Culling et al. [Speech Commun. 14, 71–96 (1994)] found that for competing synthetic vowels, masked identification thresholds were increased by reverberation only when combined with modulation of fundamental frequency (F0). The present investigation extended this finding to running speech. Speech reception thresholds (SRTs) were measured for a male voice against a single interfering female voice within a virtual room with controlled reverberation. The two voices were either (1) co-located in virtual space at 0° azimuth or (2) separately located at ±60° azimuth. In experiment 1, target and interfering voices were either normally intonated or resynthesized with a fixed F0. In anechoic conditions, SRTs were lower for normally intonated and for spatially separated sources, while, in reverberant conditions, the SRTs were all the same. In experiment 2, additional conditions employed inverted F0 contours. Inverted F0 contours yielded higher SRTs in all conditions, regardless of reverberation. The results suggest that reverberation can seriously impair listeners’ ability to exploit differences in F0 and spatial location between competing voices. The levels of reverberation employed had no effect on speech intelligibility in quiet.
The dependency of timbre on fundamental frequency
Authors: Marozeau Jeremy , de Cheveigné Alain , McAdams Stephen , Winsberg Suzanne
Published: November 2003

The dependency of the timbre of musical sounds on their fundamental frequency (F0) was examined in three experiments. In experiment I subjects compared the timbres of stimuli produced by a set of 12 musical instruments with equal F0, duration, and loudness. There were three sessions, each at a different F0. In experiment II the same stimuli were rearranged in pairs, each with the same difference in F0, and subjects had to ignore the constant difference in pitch. In experiment III, instruments were paired both with and without an F0 difference within the same session, and subjects had to ignore the variable differences in pitch. Experiment I yielded dissimilarity matrices that were similar at different F0’s, suggesting that instruments kept their relative positions within timbre space. Experiment II found that subjects were able to ignore the salient pitch difference while rating timbre dissimilarity. Dissimilarity matrices were symmetrical, suggesting further that the absolute displacement of the set of instruments within timbre space was small. Experiment III extended this result to the case where the pitch difference varied from trial to trial. Multidimensional scaling (MDS) of dissimilarity scores produced solutions (timbre spaces) that varied little across conditions and experiments. MDS solutions were used to test the validity of signal-based predictors of timbre, and in particular their stability as a function of F0. Taken together, the results suggest that timbre differences are perceived independently from differences of pitch, at least for F0 differences smaller than an octave. Timbre differences can be measured between stimuli with different F0’s.
Elastic constants of layers in isotropic laminates
Authors: Heyliger Paul R. , Ledbetter Hassel , Kim Sudook , Reimanis Ivar
Published: November 2003

The individual laminae elastic constants in multilayer laminates composed of dissimilar isotropic layers were determined using ultrasonic-resonance spectroscopy and the linear theory of elasticity. Ultrasonic resonance allows one to measure the free-vibration response spectrum of a traction-free solid under periodic vibration. These frequencies depend on pointwise density, laminate dimensions, layer thickness, and layer elastic constants. Given a material with known mass but unknown constitution, this method allows one to extract the elastic constants and density of the constituent layers. This is accomplished by measuring the frequencies and then minimizing the differences between these and those calculated using the theory of elasticity for layered media to select the constants that best replicate the frequency-response spectrum. This approach is applied to a three-layer, unsymmetric laminate of WpCu, and very good agreement is found with the elastic constants of the two constituent materials.
U.S. Navy sources and receivers for studying acoustic propagation and climate change in the ocean (L)
Authors: Spiesberger John L.
Published: November 2003

Sounds from a U.S. Navy SSQ-110A source are received at high signal-to-noise ratios at ocean-basin scales at two Sound Surveillance Systems in the Pacific. The sounds have sufficient pulse resolution to study climatic variations of temperature. The acoustic data can be understood using ray and parabolic approximations to the wave equation. Modeled internal waves decrease pulse resolution from 0.01 to 0.1 s, consistent with observations.
Sound in ecclesiastical spaces in Cordoba. Architectural projects incorporating acoustic methodology (El sonido del espacio eclesial en Cordoba. El proyecto arquitectonico como procedimiento acustico)
Authors: Suarez Rafael
Published: November 2003

This thesis is concerned with the acoustic analysis of ecclesiastical spaces, and the subsequent implementation of acoustic design methodology in architectural renovations. One begins with an adequate architectural design of specific elements (shape, materials, and textures), with the intention of elimination of acoustic deficiencies that are common in such spaces. These are those deficiencies that impair good speech intelligibility and good musical audibility. The investigation is limited to churches in the province of Cordoba and to churches built after the reconquest of Spain (1236) and up until the 18th century. Selected churches are those that have undergone architectural renovations to adapt them to new uses or to make them more suitable for liturgical use. The thesis attempts to summarize the acoustic analyses and the acoustical solutions that have been implemented. The results are presented in a manner that should be useful for the adoption of a model for the functional renovation of ecclesiastical spaces. Such would allow those involved in architectural projects to specify the nature of the sound, even though somewhat intangible, within the ecclesiastical space.

Thesis advisors: Jaime Navarro and Juan J. Sendra Copies of this thesis written in Spanish may be obtained by contacting the advisor, Jaime Navarro, E.T.S. de Arquitectura de Sevilla, Dpto. de Construcciones Arquitectonicas I, Av. Reina Mercedes, 2, 41012 Sevilla, Spain. E-mail address: jnavarro@us.es