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PubMed2004

Efficient generation of discontinuity-preserving adaptive triangulations from range images.

This paper presents an efficient technique for generating adaptive triangular meshes from range images. The algorithm consists of two stages. First, a user-defined number of points is adaptively sampled from the given range image. Those points are chosen by taking into account the surface shapes represented in the range image in such a way that points tend to group in areas of high curvature and to disperse in low-variation regions. This selection process is done through a noniterative, inherently parallel algorithm in order to gain efficiency. Once the image has been subsampled, the second stage applies a two and one half-dimensional Delaunay triangulation to obtain an initial triangular mesh. To favor the preservation of surface and orientation discontinuities (jump and crease edges) present in the original range image, the aforementioned triangular mesh is iteratively modified by applying an efficient edge flipping technique. Results with real range images show accurate triangular approximations of the given range images with low processing times.

Algorithms↗
PubMedDate not supplied

An intestinal surgery simulator: real-time collision processing and visualization.

This research work is aimed toward the development of a VR-based trainer for colon cancer removal. It enables the surgeons to interactively view and manipulate the concerned virtual organs as during a real surgery. First, we present a method for animating the small intestine and the mesentery (the tissue that connects it to the main vessels) in real-time, thus enabling user interaction through virtual surgical tools during the simulation. We present a stochastic approach for fast collision detection in highly deformable, self-colliding objects. A simple and efficient response to collisions is also introduced in order to reduce the overall animation complexity. Second, we describe a new method based on generalized cylinders for fast rendering of the intestine. An efficient curvature detection method, along with an adaptive sampling algorithm, is presented. This approach, while providing improved tessellation without the classical self-intersection problem, also allows for high-performance rendering thanks to the new 3D skinning feature available in recent GPUs. The rendering algorithm is also designed to ensure a guaranteed frame rate. Finally, we present the quantitative results of the simulations and describe the qualitative feedback obtained from the surgeons.

Algorithms↗
PubMedDate not supplied

Interactive point-based rendering of higher-order tetrahedral data.

Computational simulations frequently generate solutions defined over very large tetrahedral volume meshes containing many millions of elements. Furthermore, such solutions may often be expressed using non-linear basis functions. Certain solution techniques, such as discontinuous Galerkin methods, may even produce non-conforming meshes. Such data is difficult to visualize interactively, as it is far too large to fit in memory and many common data reduction techniques, such as mesh simplification, cannot be applied to non-conforming meshes. We introduce a point-based visualization system for interactive rendering of large, potentially non-conforming, tetrahedral meshes. We propose methods for adaptively sampling points from non-linear solution data and for decimating points at run time to fit GPU memory limits. Because these are streaming processes, memory consumption is independent of the input size. We also present an order-independent point rendering method that can efficiently render volumes on the order of 20 million tetrahedra at interactive rates.

Journal Article↗
PubMed2000

Hierarchical Bayes estimation of hunting success rates with spatial correlations.

A Bayesian hierarchical generalized linear model is used to estimate hunting success rates at the subarea level for postseason harvest surveys. The model includes fixed week effects, random geographic effects, and spatial correlations between neighboring subareas. The computation is done by Gibbs sampling and adaptive rejection sampling techniques. The method is illustrated using data from the Missouri Turkey Hunting Survey in the spring of 1996. Bayesian model selection methods are used to demonstrate that there are significant week differences and spatial correlations of hunting success rates among counties. The Bayesian estimates are also shown to be quite robust in terms of changes of hyperparameters.

Animals↗
PubMed1990

Effect of frequent milkings on milk NAGase, plasmin, trypsin inhibitory capacity and the quality of whey as the growth medium for mastitis pathogens.

Unequal milking intervals affected milk somatic cell count and N-acetyl-beta-D-glucosaminidase (NAGase) activity. The total daily output of milk NAGase and plasmin decreased, if quarters were emptied frequently during the day. Mastitis pathogens showed stimulated growth in whey prepared from filled quarters as compared with growth in whey from quarters emptied frequently during the day. The quality of whey as growth medium for mastitis pathogens paralleled plasmin activity in respective milk samples. Adaptation of mastitis pathogens to grow in whey had an enhancing effect on bacterial growth during subsequent inoculations in whey. Bacteria probably "learn" to overcome the effect from endogenous antibacterial factors and to use nutrients present in whey.

Acetylglucosaminidase↗
PubMed2005

Modeling the articulatory space using a hypercube codebook for acoustic-to-articulatory inversion.

Acoustic-to-articulatory inversion is a difficult problem mainly because of the nonlinearity between the articulatory and acoustic spaces and the nonuniqueness of this relationship. To resolve this problem, we have developed an inversion method that provides a complete description of the possible solutions without excessive constraints and retrieves realistic temporal dynamics of the vocal tract shapes. We present an adaptive sampling algorithm to ensure that the acoustical resolution is almost independent of the region in the articulatory space under consideration. This leads to a codebook that is organized in the form of a hierarchy of hypercubes, and ensures that, within each hypercube, the articulatory-to-acoustic mapping can be approximated by means of a linear transform. The inversion procedure retrieves articulatory vectors corresponding to acoustic entries from the hypercube codebook. A nonlinear smoothing algorithm together with a regularization technique is then used to recover the best articulatory trajectory. The inversion ensures that inverse articulatory parameters generate original formant trajectories with high precision and a realistic sequence of the vocal tract shapes.

Algorithms↗
PubMed1993

Where plants make oxygen: a structural model for the photosynthetic oxygen-evolving manganese cluster.

In the photosynthetic evolution of oxygen, water oxidation occurs at a catalytic site that includes four manganese atoms together with the essential cofactors, the calcium and chlorine ions. A structural model and a determination of the manganese oxidation states based on x-ray absorption spectroscopy are presented. The salient features, in both higher plants and cyanobacteria, are a pair of di-mu-oxo bridged manganese binuclear clusters linked by a mono-mu-oxo bridge, one proximal calcium atom, and one halide. In dark-adapted samples, manganese occurs in oxidation states (III) and (IV). Data from oriented membranes display distinct dichroism, precluding highly symmetrical structures for the manganese complex.

Bridged-Ring Compounds↗
PubMed2000

Inhibition of photosynthetic electron transport by UV-A radiation targets the photosystem II complex.

We have studied the inhibition of photosynthetic electron transport by UV-A (320-400 nm) radiation in isolated spinach thylakoids. Measurements of Photosystem II (PSII) and Photosystem I activity by Clark-type oxygen electrode demonstrated that electron flow is impaired primarily in PSII. The site and mechanism of UV-A induced damage within PSII was assessed by flash-induced oxygen and thermoluminescence (TL) measurements. The flash pattern of oxygen evolution showed an increased amount of the S0 state in the dark, which indicate a direct effect of UV-A in the water-oxidizing complex. TL measurements revealed the UV-A induced loss of PSII centers in which charge recombination between the S2 state of the water oxidizing complex and the semireduced Q(A)- and Q(B)- quinone electron acceptors occur. Flash-induced oscillation of the B TL band, originating from the S2Q(B)- recombination, showed a decreased amplitude after the second flash relative to that after the first one, which is consistent with a decrease in the amount of Q(B)- relative to Q(B) in dark adapted samples. The efficiency of UV-A light in inhibiting PSII electron transport exceeds that of visible light 45-fold on the basis of equal energy and 60-fold on the basis of equal photon number, respectively. In conclusion, our data show that UV-A radiation is highly damaging for PSII, whose electron transport is affected both at the water oxidizing complex, and the binding site of the Q(B) quinone electron acceptor in a similar way to that caused by UV-B radiation.

Electron Transport↗
PubMed2002

New insights into photosynthetic oscillations revealed by two-dimensional microscopic measurements of chlorophyll fluorescence kinetics in intact leaves and isolated protoplasts.

Chlorophyll fluorescence kinetic microscopy was used to analyze photosynthetic oscillations in individual cells of leaves and in isolated leaf cell protoplasts. Four Brassicaceae species were used: Arabidopsis halleri (L.) O'Kane & Al-Shehbaz, Thlaspi fendleri (Nels.) Hitchc, Thlaspi caerulescens J.&C. Presl and Thlaspi ochroleucum Boiss et Helder. With the latter two, the measurements were extended also to isolated protoplasts. The oscillations were induced under the microscope by exposing dark-adapted samples to actinic irradiance. Detailed analysis of the induced transients revealed that they consist of several processes oscillating with different frequencies and not only one component as reported earlier. Furthermore, it was found that most of these processes are controlled inside each individual cell. This was shown by differences in oscillations in neighboring cells and protoplasts that share a uniform intercellular environment. The frequency of the dominant oscillation frequency depended neither on irradiance nor on CO2 concentration and is, therefore, not controlled by the photosynthetic rate. Characteristic differences in the frequency spectrum and damping of oscillations have been found among the plant species examined.

Brassicaceae↗
PubMed2000

[Population projections: goals, methods, hypotheses].

Population projections generally use the component method which consists in adapting sample size by age and sex from mortality, fertility and migration hypotheses. This exercise is not always aimed a providing projection data, but may also serve to analyze factors changing in the population. Comparatively long-term demographic forecasts, particularly for mortality, can be made due to the major inertia of demographic phenomena. However, the quality of such predictions depends on the quality of knowledge of past evolution in the demographic factors and on the capacity to forecast their future evolution.

Adolescent↗
PubMed2000

Planning and rehearsal of surgical interventions in the volume model.

Visualization of 3D medical data is routinely used in a wide range of applications. However, for the planning and rehearsal of surgical interventions more sophisticated techniques for interaction have to be developed. The realistic specification and visualization of free form cuts is needed to allow the 'look and feel' close to a real dissection. The problem here is, since these cuts are not represented by intensity changes, that the gray-level-gradient-method can not be used for the estimation of surface normals. In addition, the interactive repositioning of dissected fragments has to be simulated. We have developed an extended ray-casting algorithm for visualization of object motion in the volume model. We implemented new methods for the representation, modeling and high quality rendering (subvoxel resolution) of arbitrarily shaped cut regions within the volume model. The representation is done using a dynamic data structure. This way, all operations can easily be reversed and the original object information is preserved. The modeling of cut surfaces is done in an independent data volume where the partial-volume-effect, which is the prerequisite for the gray-level-gradient method, is calculated as it would be generated by an imaging system. This way, the localization of cut surfaces at subvoxel resolution and an accurate estimation of the surface normals is achieved. The key point here is to detect if a cut surface really truncates an object or if the object has not been affected by a cutting operation. We will present an new method, called adaptive sampling which allows to determine the situation by the generation of additional sample points (when necessary) during the ray casting process. The described techniques provides the basis for simulation of surgical interventions in the voxel-model which could not be achieved with any surface-based method. We present a system for simulation and rehearsal of otosurgical approaches, where we implemented a drill-like tool with which the student lays off the route to the operating area. The key point is to not injure structures of risk such as the facial nerve. For applications like the simulation of craniofacial surgery we developed a gradual cutting tool ("virtual scalpel").

Computer Graphics↗
PubMed2001

[Diagnosis and treatment of nosocomial pneumonia: bronchial fibroscopy, protected brushing and/or bronchial lavage is indispensable].

In case of suspected nosocomial lung infection in an intensive care patient, a strictly "clinical" strategy based on the physical exam and qualitative culture of tracheal secretions has three potential drawbacks: i) Numerous patients are given unnecessary antibiotic regimens unwarranted on the sole basis of colonization of the upper airways. In addition to the high cost of such regimens, these antibiotics also have important adverse effects favoring the emergence of multiresistant strains, and in addition, considerably complicating the search for the real cause and the treatment of the fever and the new lung images. ii) This strategy exposes the patient to diagnostic errors by omission if all patients with suspected infection are not treated. iii) Finally, even if the diagnosis of pneumonia is exact, the antibiotic prescribed on the basis of necessarily imprecise information can be most inappropriate or non-optimal in many cases. It is particularly difficult or often impossible to taper off the regimen on day 3 when tracheal cultures become available since the prescription would have to cover all the germs present in the upper airways even though only certain strains are undoubtedly causing the infection in the lung parenchyma. We prefer another strategy based on systematic bronchial fibroscopy before changing the antibiotic regimen in patients presenting signs suggestive of nosocomial pneumonia. The fibroscope allows us to obtain minimally-contaminated or non-contaminated specimens of the distal lung secretions in the suspected zone using the "Wimberley" brush for a protected sample and/or bronchoalveolar lavage. Although data in the literature on the usefulness of protected brushings and bronchoalveolar lavage specimens is rather confusing due to methodological differences, all the published work confirms that these techniques do allow identification of the germs present in the lung at the time of the sampling. Thus, on the basis of the culture results, it would be possible to discontinue any unnecessary antibiotic in patients with negative samples and inversely to use the narrowest possible treatment spectrum for those with positive samples, adapting the regimen to the susceptibility pattern or identified strains. The strongest arguments favoring this invasive strategy come from a multicentric French study on 413 patients with clinically suspected nosocomial pneumonia under artificial ventilation. The results demonstrated lower mortality in the fibroscopy group associated with a major reduction in the consumption of antibiotics.

Algorithms↗
PubMed1978

Electric field-induced polarization of photosynthetic membranes and reaction centers of Rhodopseudomonas sphaeroides, strain 1760-1.

Electric fields of 10(5) V/cm cause the polarization of chromatophore and reaction center films prepared from photosynthesizing purple bacteria. Photosynthetic pigments, and in particular carotenoids, the absorption spectra of which are changed in response to electric fields (electrochromism), may serve as intrinsic indicators of the development of a polarized state. Polarization occurs due to changes in the orientation and the spatial position of different charged groups and particles. The field-induced polarized state can be fixed by exposure to low temperature (-120 degrees C). On being heated, the system relaxes to the initial state and this can be seen as a thermodepolarization current in an electric circuit. The effects of hydration, chemical modification or heat treatment on thermodepolarization current indicate the involvement of macromolecular components in the formation of a polarized state. In light-adapted samples the polarization effect is markedly greater, indicating that conformational changes occur during the primary photoact. It is assumed that the polarization of the reaction centers during electron transfer might be involved in the stabilization of separated charges and in the storage of energy.

Bacterial Chromatophores↗
PubMedDate not supplied

[Polarization of photosynthetic membranes and reaction centers of Rhodopseudomonas sphaeroides 1760-1 in an external electrical field].

Electric fields as high as 10(5) V/cm cause polarization of chromatophores and reaction centre films prepared from photosynthesizing bacteria. Photosynthetic pigments, carotenoids in particular, the absorption spectra of which are changed in response to electric fields, may serve as an intrinsic indicator of the development of a polarized state. Polarization occurs due to changes in orientation and spacial position of different charge groups and particles. The field-induced polarized state can be fixed up by exposure to low temperature (-120 degrees C). While heating the system relaxes to the initial state and this can be seen as a current in an electric circuit. The effects of hydration, chemical modification or heat treatment on current indicate the involvement of macromolecule components in the formation of a polarized state, In light-adapted samples the polarization effect is markedly greater and this can indicate that conformational changes occur during the primary photoact. It is supposed that polarization might be implicated in the stabilization of separated charges and in the storage of energy.

Bacterial Chromatophores↗
PubMed1986

Photochromism of halorhodopsin. cis/trans isomerization of the retinal around the 13-14 double bond.

The isomeric composition of retinal in membrane-bound and in purified but detergent-free, dark-adapted halorhodopsin was found to be about 70% 13-cis and 30% all-trans. Any illumination increased the all-trans content relative to the dark-adapted state, but blue illumination shifted the isomeric composition more toward all-trans while red illumination of blue-adapted samples shifted it more toward 13-cis. In the presence of chloride this photoisomerization caused the kind of photochromic behavior reported earlier in Smith, S. O., Marvin, M. J., Bogomolni, R. A., and Mathies, R. A. (1984) J. Biol. Chem. 259, 12326-12329, i.e. blue light caused the absorption maximum to move toward longer wavelengths and red light reversed the shift. Only the all-trans chromophore exhibited the complete photocycle described earlier in detergent-solubilized halorhodopsin, and this was the form that could be associated with light-driven chloride transport activity in cell envelope vesicles. In the absence of chloride the spectroscopic changes caused by illumination were much smaller. Reconstitution of bleached preparations with 13-cis- and all-trans-retinal, in the presence and absence of chloride, confirmed that the difference between the absorption maxima of the two isomeric forms of the chromophore is affected by chloride: 13-cis-halorhodopsin absorbs at about 567-568 nm with and without chloride, and the all-trans pigment absorbs near 568 nm in the absence of chloride, but at 578 nm in its presence. The simplest explanation of this finding is that most of the red-shift which accompanies the 13-cis----all-trans transition originates from electrostatic interaction of the retinal with chloride bound in its vicinity.

Bacteriorhodopsins↗
PubMed1979

A concept for stereological investigation of rat kidney.

An attempt is presented to adapt sampling procedures for stereological investigation of rat kidney. The proposed experimental design considers the zonal construction, in particular the structural and osmotic features of this organ. Every zone is treated as an own entity inregard to sample collection. In order to uncover possibly existing preferential orientation of structures the application of two mutually perpendicular section planes is recommended. Furthermore a method is described to determine absolute volumes and surface of structural components.

Animals↗
PubMed1994

Flash-induced absorption spectroscopy studies of copper interaction with photosystem II in higher plants.

Measurements of flash-induced absorption changes at 325, 436, and 830 nm and of oxygen evolution were performed in order to analyze in detail the inhibition of photosystem II (PS II) by Cu(II) in PS II membrane fragments from spinach. (a) The kinetics of P680+ reduction become markedly slower in the presence of 100 microM CuSO4. (b) The CuSO4-induced kinetics of P680+ reduction are dominated by a 140-160-microsecond decay. (c) The extent of these 140-160-microsecond kinetics, normalized to the overall decay, remains virtually unaffected by addition of the exogenous PS II donor, NH2OH. (d) In thoroughly dark-adapted samples the CuSO4-induced 140-160-microsecond kinetics are already observed after the first flash and remain unchanged by a train of excitation flashes. (e) The extent of P680+ and QA- formation under repetitive flash excitation is not diminished by addition of 100 microM CuSO4. (f) The induction of microsecond kinetics of P680+ reduction at the expense of ns kinetics and the inhibition of the saturation rate of oxygen evolution exhibit the same dependence on CuSO4 concentration. (g) CuSO4 also transforms the 10-20-microsecond reduction of P680+ by TyrZ in Tris-washed PS II membrane fragments into 140-160-microsecond kinetics without any effect on the extent of flash-induced P680+ formation. These results unambiguously show that Cu(II) does not affect the charge separation (P680+QA-), but instead specifically modifies TyrZ and/or its micro environment so that the electron transfer to P680+ becomes blocked.

Copper↗
PubMed1992

An adapter for defined sample volumes makes it possible to count absolute particle numbers in flow cytometry.

A device is described which makes it possible to count absolute particle (cell) numbers per volume by flow cytometry. It can easily by adapted to several types of flow cytometers, especially to the Coulter EPICS V and EPICS 750 series. A volume adapter has been installed in place of the normal sample handling system without any further modifications of the instrument or the data acquisition program. The adapter consists of a special pipette with two opto-electronic detectors for the beginning and end of the measuring period. These switch on/off a shutter for the illuminating laser beam so that acquisition of the data is controlled indirectly. Sample volumes of 50 microliters were measured at flow rates up to 10(3) particles/s. Calibration beads as well as blood cells were enumerated according to FALS (forward angle light scatter), to SSC (90 degrees light scatter), and to fluorescence parameters. The results were compared to the evaluation made on a Coulter counter or in a Neubauer chamber of a light microscope. Using a concentration of 1 x 10(5)-5 x 10(5) particles/ml, the absolute numbers of particles were determined with a high reproducibility and an estimated error rate of 2-5%.

Antibodies, Monoclonal↗