Tools for fluid simulation control in computer graphics

L’animation basée sur la physique peut générer des systèmes aux comportements complexes et réalistes. Malheureusement, contrôler de tels systèmes est une tâche ardue. Dans le cas de la simulation de fluide, le processus de contrôle est particulièrement complexe. Bien que de nombreuses méthodes et outils ont été mis au point pour simuler et faire le rendu de fluides, trop peu de méthodes offrent un contrôle efficace et intuitif sur une simulation de fluide. Étant donné que le coût associé au contrôle vient souvent s’additionner au coût de la simulation, appliquer un contrôle sur une simulation à plus haute résolution rallonge chaque itération du processus de création. Afin d’accélérer ce processus, l’édition peut se faire sur une simulation basse résolution moins coûteuse. Nous pouvons donc considérer que la création d’un fluide contrôlé peut se diviser en deux phases: une phase de contrôle durant laquelle un artiste modifie le comportement d’une simulation basse résolution, et une phase d’augmentation de détail durant laquelle une version haute résolution de cette simulation est générée. Cette thèse présente deux projets, chacun contribuant à l’état de l’art relié à chacune de ces deux phases. Dans un premier temps, on introduit un nouveau système de contrôle de liquide représenté par un modèle particulaire. À l’aide de ce système, un artiste peut sélectionner dans une base de données une parcelle de liquide animé précalculée. Cette parcelle peut ensuite être placée dans une simulation afin d’en modifier son comportement. À chaque pas de simulation, notre système utilise la liste de parcelles actives afin de reproduire localement la vision de l’artiste. Une interface graphique intuitive a été développée, inspirée par les logiciels de montage vidéo, et permettant à un utilisateur non expert de simplement éditer une simulation de liquide. Dans un second temps, une méthode d’augmentation de détail est décrite. Nous proposons d’ajouter une étape supplémentaire de suivi après l’étape de projection du champ de vitesse d’une simulation de fumée eulérienne classique. Durant cette étape, un champ de perturbations de vitesse non-divergent est calculé, résultant en une meilleure correspondance des densités à haute et à basse résolution. L’animation de fumée résultante reproduit fidèlement l’aspect grossier de la simulation d’entrée, tout en étant augmentée à l’aide de détails simulés.Physics-based animation can generate dynamic systems of very complex and realistic behaviors. Unfortunately, controlling them is a daunting task. In particular, fluid simulation brings up particularly difficult problems to the control process. Although many methods and tools have been developed to convincingly simulate and render fluids, too few methods provide efficient and intuitive control over a simulation. Since control often comes with extra computations on top of the simulation cost, art-directing a high-resolution simulation leads to long iterations of the creative process. In order to shorten this process, editing could be performed on a faster, low-resolution model. Therefore, we can consider that the process of generating an art-directed fluid could be split into two stages: a control stage during which an artist modifies the behavior of a low-resolution simulation, and an upresolution stage during which a final high-resolution version of this simulation is driven. This thesis presents two projects, each one improving on the state of the art related to each of these two stages. First, we introduce a new particle-based liquid control system. Using this system, an artist selects patches of precomputed liquid animations from a database, and places them in a simulation to modify its behavior. At each simulation time step, our system uses these entities to control the simulation in order to reproduce the artist’s vision. An intuitive graphical user interface inspired by video editing tools has been developed, allowing a nontechnical user to simply edit a liquid animation. Second, a tracking solution for smoke upresolution is described. We propose to add an extra tracking step after the projection of a classical Eulerian smoke simulation. During this step, we solve for a divergence-free velocity perturbation field resulting in a better matching of the low-frequency density distribution between the low-resolution guide and the high-resolution simulation. The resulting smoke animation faithfully reproduces the coarse aspect of the low-resolution input, while being enhanced with simulated small-scale details

From structure to function: possible biological roles of a new widespread protein family binding hydrophobic ligands and displaying a nucleotide binding site

AbstractA cytosolic 21–23 kDa protein isolated from bovine brain was demonstrated to bind hydrophobic ligands, particularly phosphatidylethanolamine. The protein was encountered in numerous tissues of several species. High expression of the mRNA encoding the 21–23 kDa protein was found in rat testes. Immunohistochemical studies showed the presence of the 21–23 kDa protein in the elongated spermatids and epididymal fluid of rat testis and in brain oligodendrocytes of developing rats. As the bovine, human and rat brain 21–23 kDa proteins had only few sequence homologies with already known proteins, it was concluded that they belong to a new protein family. In order to get additional information on the structural features of the 21–23 kDa protein, we built a molecular model which displayed a nucleotide binding site. The affinity of the bovine brain 21–23 kDa protein towards nucleotides as well as its association with cytosolic proteins and small GTP-binding proteins were demonstrated. Recently, significant sequence homologies were found with an antigen from Onchocerca volvulus, a fruit fly odorant-binding protein and the yeast protein TFS1 which is a dosage-dependant suppressor of CDC25 mutations. A positive regulation of RAS is carried out by CDC25 product which facilitates the GDP/GTP exchange on RAS proteins. These results imply that 21–23 kDa proteins function in oxidoreduction reactions and signal mechanisms during cell growth and maturation

Vocal tract settings in speakers suffering from obstructive sleep apnea síndrome

Automatic systems based on speech signal analysis for the early dete ction of obstructive sleep apnea (OSA) have achieved fairly high performance rates in recent years. However, a satisfactory explanation of these results has not been available. This presentation aims at explaining via an examination of the long-term spectra of OSA patients and normal control speakers these systems’ ability to discover OSA speakers on the base of all-purpose cepstral coefficients. An in terpretation of the long- term spectra in terms of the underlying tract settings suggests that the speech of OSA patients is characterized by a pharyngeal narrowing that may be captured by acoustic cues of the spectral contour of windowed speech frames. A novel interpretation of long-term spectra in terms of the first principal component of the temporal sequence of short-term amplitude-spectra is also discussed

Impact of vocal load on breathiness: Perceptual evaluation

peer reviewedObjectives: To evaluate the impact on voice of 2 hours of continuous oral reading. Methods: Fifty normophonic women underwent two sessions of voice loading in which the required intensity level varied: 60-65 dB(A) for the first session, and 70-75 dB(A) for the second session. Ten expert judges evaluated the breathiness of one sentence recorded before and after each loading session. Pairs of stimuli were presented randomly to the judges, who were asked to designate the breathiest sample. Results: A significant decrease in breathiness was observed following both sessions, suggesting an improvement of voice subsequent to loading. When comparing the two intensity levels, no difference was found for breathiness after vocal loading

Voicing quantification is more relevant than period perturbation in substitution voices: an advanced acoustical study

Quality of substitution voicing—i.e., phonation with a voice that is not generated by the vibration of two vocal folds—cannot be adequately evaluated with routinely used software for acoustic voice analysis that is aimed at ‘common’ dysphonias and nearly periodic voice signals. The AMPEX analysis program (Van Immerseel and Martens) has been shown previously to be able to detect periodicity in irregular signals with background noise, and to be suited for running speech. The validity of this analysis program is first tested using realistic synthesized voice signals with known levels of cycle-to-cycle perturbations and additive noise. Second, exhaustive acoustic analysis is performed of the voices of 116 patients surgically treated for advanced laryngeal cancer and recorded in seven European academic centers. All of them read out a short phonetically balanced passage. Patients were divided into six groups according to the oscillating structures they used to phonate. Results show that features related to quantification of voicing enable a distinction between the different groups, while the features reporting F0-instability fail to do so. Acoustic evaluation of voice quality in substitution voices thus best relies upon voicing quantification

Structural relationship between link proteins and proteoglycan monomers

AbstractStructural homologies between link proteins and proteoglycan monomers are demonstrated. A possible redundancy in the proteoglycan monomers structure is discussed and the link proteins domains homologous to other proteins are specified

Suppression of Raf-1 kinase activity and MAP kinase signalling by RKIP

Raf-1 phosphorylates and activates MEK-1, a kinase that activates the extracellular signal regulated kinases (ERK). This kinase cascade controls the proliferation and differentiation of different cell types. Here we describe a Raf-1-interacting protein, isolated using a yeast two-hybrid screen. This protein inhibits the phosphorylation and activation of MEK by Raf-1 and is designated RKIP (Raf kinase inhibitor protein). In vitro, RKIP binds to Raf-1, MEK and ERK, but not to Ras. RKIP co-immunoprecipitates with Raf-1 and MEK from cell lysates and colocalizes with Raf-1 when examined by confocal microscopy. RKIP is not a substrate for Raf-1 or MEK, but competitively disrupts the interaction between these kinases. RKIP overexpression interferes with the activation of MEK and ERK, induction of AP-1-dependent reporter genes and transformation elicited by an oncogenically activated Raf-1 kinase. Downregulation of endogenous RKIP by expression of antisense RNA or antibody microinjection induces the activation of MEK-, ERK- and AP-1-dependent transcription. RKIP represents a new class of protein-kinase-inhibitor protein that regulates the activity of the Raf/MEK/ERK modul

The Supervision of Speech Production

Introduction Since the emergence of phonology as a component within the generative paradigm of linguistics there has been discussion concerning how it relates to phonetics. At least two views of the relationship are possible: € Phonology describes the same data as phonetics, but whereas phonetics models physical detail phonology models abstract relationships holding between units within the data. These units are defined within the general framework of linguistic theory. € Phonology stands logically prior to phonetics, and the output of its processes comprises the input to phonetics. Phonetics itself is a processing component producing an output. The model can be regarded as static, involving no temporal relationship (the usual view in linguistics), or it can be regarded as dynamic. The dynamic view is often taken when the theory is used to support work in an allied area, for example in speech technology, where temporal as well as logical relationships between processes are important. It is usually understood that phonetic processes are of little concern to linguistics, and that by the output of phonology all linguistic processing is complete. Phonetic realisation of phonological 'requirements' is thought of as a passive process involving no cognitive processing, and introducing nothing new of linguistic consequence or interest. For example, phonologists working on language acquisition are interested in the phonetic constraints on what can be acquired by a child, but are not concerned with the detail of phonetic processes. The most extreme form of this position would be that speech processing of a cognitive nature falls within the province of phonology, but that all physical processing falls within the province of phonetics. Since, by definition, language is a cognitive system it can have nothing formal to do with phonetics, except in its trivial realisational rôle. There has recently been a trend toward a more phonetic approach to phonology, 1,2 and a greater awareness among phoneticians of the abstractions ofphonology3 and why they are necessary. This paper will consider how ARTICULATORY PHONOLOGY might handle some phonetic data, and attempt to deal with some problems that the data points up in the theory

The biology of a prostate cancer metastasis suppressor protein: Raf kinase inhibitor protein

Raf kinase inhibitor protein (RKIP) was originally identified as a protein that bound membrane phospholipids and was named phosphatidylethanolamine binding protein-2 (PEBP-2). RKIP was than identified as a protein that bound Raf and blocked its ability to phosphorylate MEK, thus earning its new name of RKIP. Subsequent to identification of its role in the Raf:MEK pathway, RKIP has been demonstrated to regulate several other signaling pathways including G-protein signaling and NF-ΚB signaling. Its involvement in several signaling pathways has engendered RKIP to contribute to several physiological processes including membrane biosynthesis, spermatogenesis, neural development, and apoptosis. RKIP is expressed in many tissues including brain, lung, and liver and thus, dysregulation of RKIP expression or function has potential to contribute to pathophysiology in these tissues. Loss of RKIP expression in prostate cancer cells confers a metastatic phenotype on them. Additionally, restoration of RKIP expression in a metastatic prostate cancer cell line does not effect primary tumor growth, but it does inhibit prostate cancer metastasis. These parameters identify RKIP as a metastasis suppressor gene. In this review, the biology and pathophysiology of RKIP is described. © 2004 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34907/1/20169_ftp.pd

Ligand Binding Study of Human PEBP1/RKIP: Interaction with Nucleotides and Raf-1 Peptides Evidenced by NMR and Mass Spectrometry

Background Human Phosphatidylethanolamine binding protein 1 (hPEBP1) also known as Raf kinase inhibitory protein (RKIP), affects various cellular processes, and is implicated in metastasis formation and Alzheimer's disease. Human PEBP1 has also been shown to inhibit the Raf/MEK/ERK pathway. Numerous reports concern various mammalian PEBP1 binding ligands. However, since PEBP1 proteins from many different species were investigated, drawing general conclusions regarding human PEBP1 binding properties is rather difficult. Moreover, the binding site of Raf-1 on hPEBP1 is still unknown. Methods/Findings In the present study, we investigated human PEBP1 by NMR to determine the binding site of four different ligands: GTP, FMN, and one Raf-1 peptide in tri-phosphorylated and non-phosphorylated forms. The study was carried out by NMR in near physiological conditions, allowing for the identification of the binding site and the determination of the affinity constants KD for different ligands. Native mass spectrometry was used as an alternative method for measuring KD values. Conclusions/Significance Our study demonstrates and/or confirms the binding of hPEBP1 to the four studied ligands. All of them bind to the same region centered on the conserved ligand-binding pocket of hPEBP1. Although the affinities for GTP and FMN decrease as pH, salt concentration and temperature increase from pH 6.5/NaCl 0 mM/20°C to pH 7.5/NaCl 100 mM/30°C, both ligands clearly do bind under conditions similar to what is found in cells regarding pH, salt concentration and temperature. In addition, our work confirms that residues in the vicinity of the pocket rather than those within the pocket seem to be required for interaction with Raf-1.METASU