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At least 829 records · Page 46Linked to original sources
PubMed1999

Flow properties of fast three-dimensional sequences for MR angiography.

To reduce the scan time of time of flight or phase contrast angiography sequences, fast three-dimensional k-space trajectories can be employed. The best 3D trajectory depends on tolerable scan time, readout time, geometric flexibility, flow/motion properties and others. A formalism for flow/motion sensitivity comparison based on the velocity k-space behavior is presented. It consists in finding the velocity k-space position as a function of the spatial k-space position. The trajectories are compared graphically by their velocity k-space maps, with simulations and with an objective computed index. The flow/motion properties of various 3D trajectories (cones, spiral-pr hybrid, spherical stack of spirals, 3DFT, 3D echo-planar, and shells) were determined. In terms of flow/motion sensitivity the cones trajectory is the best, however, it is difficult to use it for anisotropic resolutions or fields of view. Tolerating more flow sensitivity, the stack of spirals trajectory offers more geometric flexibility.

Blood Flow Velocity↗
PubMed1990

Color regulation in the archaebacterial phototaxis receptor phoborhodopsin (sensory rhodopsin II).

Phoborhodopsin, a repellent phototaxis receptor in Halobacterium halobium, exhibits vibrational fine structure, a feature that has not been identified for any other rhodopsin pigment at physiological temperatures. This conclusion follows form analysis of the absorption properties of the pigment in H. halobium membranes containing native retinal and an array of retinal analogues. The absorption spectrum of the native pigment has a maximum at 487 nm with a pronounced shoulder at 460 nm; however, the bandwidth is that expected for a single retinylidene species. Gaussian band-shape simulation with a spacing corresponding to the vibrational frequencies of polyene stretching modes reproduces the structured absorption spectra of native pigment as well as of analogue phoborhodopsin. Absorption shifts produced by a series of dihydroretinal and other retinal analogues strongly indicate that the dominant factor regulating the color of the pigment is planarization of the retinal ring with respect to the polyene chain.

Archaeal Proteins↗
PubMed2005

How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study.

We have applied the Transition Path Sampling algorithm to the reaction catalyzed by the enzyme Lactate Dehydrogenase. This study demonstrates the ease of scaling Transition Path Sampling for applications on many degree of freedom systems, whose energy surface is a complex terrain of valleys and saddle points. As a Monte Carlo importance sampling method, transition path sampling is capable of surmounting barriers in path phase space and focuses simulation on the rare event of enzyme catalyzed atom transfers. Generation of the transition path ensemble, for this reaction, resolves a paradox in the literature in which some studies exposed the catalytic mechanism of hydride and proton transfer by lactate dehydrogenase to be concerted and others stepwise. Transition path sampling has confirmed both mechanisms as possible paths from reactants to products. With the objective to identify a generalized, reduced reaction coordinate, time series of both donor-acceptor distances and residue distances from the active site have been examined. During the transition from pyruvate to lactate, residues located behind the transferring hydride collectively compress toward the active site causing residues located behind the hydride acceptor to relax away. It is demonstrated that an incomplete compression/relaxation transition across the donor-acceptor axis compromises the reaction.

Catalysis↗
PubMed2004

Network structures of polyhedral oligomeric silsesquioxane based nanocomposites: a Monte Carlo study.

The network structures of polyhedral oligomeric silsesquioxane based nanocomposites are studied by continuous-space Monte Carlo simulations. The nanoporous network contains intercubic pores and mesopores which can be clearly identified in this work. In terms of degree of cross linking and pore size distribution (PSD), effects of linker length, tether rigidity, and number of reactive tethers are examined. It is found that the extent of cross linking as well as the intercubic pore size of the network increases as linker length increases which are consistent with experimental findings. However, the mesopores appear to shift to a smaller radii regime for networks with longer linkers. Networks with rigid tethers contain lots of free linkers, thus, low cross linking density and narrow PSD are observed. On the other hand, reduction of the reactive tethers shows an insignificant effect on the degree of cross linking of the system. The fact that the intercubic pore size increases as the number of reactive tethers decreases causes the nanobuilding blocks to possess larger free volumes and distribute themselves more evenly throughout the system. As a result, it reduces the possibility of forming large mesopores.

Journal Article↗
PubMed2004

Analysis of the conformational dependence of mass-metric tensor determinants in serial polymers with constraints.

It is well known that mass-metric tensor determinants det(G(s)) influence the equilibrium statistics and the rates of conformational transitions for polymers with constrained bond lengths and bond angles. It is now standard practice to include a Fixman-style compensating potential of the form U(c)(q(s)) proportional, variant(-k(B)T/2)ln[det(G(s))] as part of algorithms for torsional space molecular dynamics. This elegant strategy helps eliminate unwarranted biases that arise due to the imposition of holonomic constraints. However, the precise nature and extent of variation of det(G(s)) and hence ln[det(G(s))] with chain conformation and chain length has never been quantified. This type of analysis is crucial for understanding the nature of the conformational bias that the introduction of a Fixman potential aims to eliminate. Additionally, a detailed analysis of the conformational dependence of det(G(s)) will help resolve ambiguities regarding suggestions for incorporating terms related to det(G(s)) in the design of move sets in torsional space Monte Carlo simulations. In this work, we present results from a systematic study of the variation of det(G(s)) for a serial polymer with fixed bond lengths and bond angles as a function of chain conformation and chain length. This analysis requires an algorithm designed for rapid computation of det(G(s)) which simultaneously allows for a physical/geometric interpretation of the conformational dependence of det(G(s)). Consequently, we provide a detailed discussion of our adaptation of an O(n) algorithm from the robotics literature, which leads to simple recursion relations for direct evaluation of det(G(s)). Our analysis of the conformational dependence of det(G(s)) yields the following insights. (1) det(G(s)) is maximized for spatial conformers and minimized for planar conformations. (2) Previous work suggests that it is logical to expect that the conformational dependence of det(G(s)) becomes more pronounced with increase in chain length. Confirming this expectation, we provide systematic quantification of the nature of this dependency and show that the difference in det(G(s)) between spatial and planar conformers, i.e., between the maxima and minima of det(G(s)) grows systematically with chain length. Finally, we provide a brief discussion of implications of our analysis for the design of move sets in Monte Carlo simulations.

Journal Article↗
PubMed2006

On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data.

We propose a method for calculating absolute free energies from Monte Carlo or molecular-dynamics data. The method is based on the identity that expresses the partition function Q as a Boltzmann average: 1Q=w(p,x)exp[betaH(p,x)], where w(p,x) is an arbitrary weight function such that its integral over the phase space is equal to 1. In practice, to minimize statistical errors the weight function is chosen such that the regions of the phase space where sampling statistics are poor are excluded from the average. The "ideal" weight function would be the equilibrium phase-space density exp[-betaH(p,x)]Q itself. We consider two methods for constructing the weight function based on different estimates of the equilibrium phase-space density from simulation data. In the first method, it is chosen to be a Gaussian function, whose parameters are obtained from the covariance matrix of the atomic coordinates. In the second, a clustering algorithm is used to attempt partitioning the data into clusters corresponding to different basins of attraction visited by the system. The weight function is then constructed as a superposition of Gaussians calculated for each cluster separately. We show that these strategies can be used to improve upon previous methods of estimating absolute entropies from covariance matrices.

Algorithms↗
PubMed1999

Time-resolved analysis and visualization of dynamic processes in living cells.

Recent development of in vivo microscopy techniques, including green fluorescent proteins, has allowed the visualization of a wide range of dynamic processes in living cells. For quantitative and visual interpretation of such processes, new concepts for time-resolved image analysis and continuous time-space visualization are required. Here, we describe a versatile and fully automated approach consisting of four techniques, namely highly sensitive object detection, fuzzy logic-based dynamic object tracking, computer graphical visualization, and measurement in time-space. Systematic model simulations were performed to evaluate the reliability of the automated object detection and tracking method. To demonstrate potential applications, the method was applied to the analysis of secretory membrane traffic and the functional dynamics of nuclear compartments enriched in pre-mRNA splicing factors.

Animals↗
PubMed1999

Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods.

Ras farnesyltransferase catalyzes the carboxyl-terminal farnesylation of Ras as well as other proteins involved in signal transduction processes. Previous studies demonstrated that its inhibition suppresses the activity of Ras transformed phenotypes in cultured cells, causing tumor regression in animal models. This observation led to the consideration of farnesyltransferase as a target for cancer therapy. In the present work we report the results of a computational study aimed at assessing the bioactive conformation of the peptide Cys-Val-Phe-Met, known to be the minimum peptide sequence that inhibits farnesyltransferase. For this purpose the conformational preferences of four analogs of the peptide were assessed by means of thorough searches of their respective conformational spaces, using a simulated annealing protocol as sampling technique. Specifically, two active analogs: Cys-Val-Tic-Met and Cys-Val-psi(CH2NH)Tic-Met and two inactive analogs: Cys-Val-Tic-psi(CH2NH)Met and Cys-Val-Aic-Met were selected for the present study. Low energy conformations of the four analogs were classified according to their structural motifs. The putative bioactive conformation of the minimum farnesyltransferase recognition motif was assessed by cross-comparison of the different classes of conformations obtained for the two active and the two inactive analogs. The putative bioactive conformation is characterized by two structural motifs: i) a C14 pseudo-ring stabilized by a hydrogen bond between the amino group of Cys1 and the carboxylate group of Met4 and a C11 pseudo-ring involving the residues Cys1 and Tic3. In addition, the thiol group of Cys1 side chain of the bioactive conformation points to the carboxylate moiety of Met4.

Algorithms↗
PubMed2004

LOR-OSEM: statistical PET reconstruction from raw line-of-response histograms.

Iterative statistical reconstruction methods are becoming the standard in positron emission tomography (PET). Conventional maximum-likelihood expectation-maximization (MLEM) and ordered-subsets (OSEM) algorithms act on data which have been pre-processed into corrected, evenly-spaced histograms; however, such pre-processing corrupts the Poisson statistics. Recent advances have incorporated attenuation, scatter and randoms compensation into the iterative reconstruction. The objective of this work was to incorporate the remaining pre-processing steps, including arc correction, to reconstruct directly from raw unevenly-spaced line-of-response (LOR) histograms. This exactly preserves Poisson statistics and full spatial information in a manner closely related to listmode ML, making full use of the ML statistical model. The LOR-OSEM algorithm was implemented using a rotation-based projector which maps directly to the unevenly-spaced LOR grid. Simulation and phantom experiments were performed to characterize resolution, contrast and noise properties for 2D PET. LOR-OSEM provided a beneficial noise-resolution tradeoff, outperforming AW-OSEM by about the same margin that AW-OSEM outperformed pre-corrected OSEM. The relationship between LOR-ML and listmode ML algorithms was explored, and implementation differences are discussed. LOR-OSEM is a viable alternative to AW-OSEM for histogram-based reconstruction with improved spatial resolution and noise properties.

Algorithms↗
PubMed2026

BaGGLS: a Bayesian shrinkage framework for interpretable modeling of interactions in high-dimensional biological data.

MOTIVATION: Biological data is often high dimensional, noisy, and governed by complex interactions among sparse signals. This poses major challenges for interpretability and reliable feature selection. Tasks such as identifying motif interactions in genomics exemplify these difficulties, as only a small subset of biologically relevant features (e.g. motifs) are typically active, and their effects are often non-linear and context-dependent. While statistical approaches often result in more interpretable models, deep learning models have proven effective in modeling complex interactions and prediction accuracy, yet their black-box nature limits interpretability. RESULTS: We introduce BaGGLS, a flexible and interpretable probabilistic binary regression model designed for high-dimensional biological inference involving feature interactions. BaGGLS incorporates a Bayesian group global-local shrinkage prior, aligned with the group structure introduced by interaction terms. This prior encourages sparsity while retaining interpretability, helping to isolate meaningful signals and suppress noise. To enable scalable inference, we employ a partially factorized variational approximation that captures posterior skewness and supports efficient learning even in large feature spaces. In extensive simulations, we compare BaGGLS to frequentist probit regressions (unconstrained and with L1-penalty) as well as a probit model with Markov Chain Monte Carlo (MCMC) sampling under a horseshoe prior. We can show that BaGGLS outperforms the other methods with regard to interaction detection and is many times faster than MCMC sampling under the horseshoe prior. We also demonstrate the usefulness of BaGGLS in the context of interaction discovery from motif scanner outputs (e.g. Find Individual Motif Occurrences (FIMO)) and noisy attribution scores from deep learning models. This shows that BaGGLS is a promising approach for uncovering biologically relevant interaction patterns, with potential applicability across a range of high-dimensional tasks in computational biology. AVAILABILITY: Code is available at gitlab.com/dacs-hpi/baggls.

Bayes Theorem↗
PubMed1986

Ciprofloxacin, azlocillin, ceftizoxime and amikacin alone and in combination against gram-negative bacilli in an infected chamber model.

Ciprofloxacin, azlocillin, ceftizoxime, and amikacin were studied alone and in combination against six Enterobacteriaceae and six strains of Pseudomonas aeruginosa in an infected chamber model in rabbits simulating a closed space infection. In-vivo results were compared with in-vitro tests of inhibition, killing and synergy. Ciprofloxacin was the most effective single agent, with efficacy against five of the six Enterobacteriaceae when used in low doses, and two of the six pseudomonads when used in high doses. The development of in-vitro resistance to ciprofloxacin was observed during therapy in strains which failed to be eradicated. Ciprofloxacin and azlocillin together was the most effective regimen, with efficacy against eleven of the twelve strains. Synergy, as determined by chequerboard testing, did not correlate with in-vivo outcome. Unlike mezlocillin, azlocillin, ceftizoxime or amikacin, MIC testing of ciprofloxacin was predictive of in-vivo success.

Amikacin↗
PubMed1997

Volume kinetics of Ringer solution, dextran 70, and hypertonic saline in male volunteers.

BACKGROUND: A knowledge of the distribution of different fluids given by intravenous infusion is basic to the understanding of the effects of fluid therapy. Therefore, a mathematical model was tested to analyze the volume kinetics of three types of fluids. METHODS: The authors infused 25 ml/kg of Ringer acetate solution, 5 ml/kg of 6% dextran 70 in 0.9% NaCl, and 3 ml/kg of 7.5% NaCl over 30 min in 8 male volunteers aged from 25 to 36 years (mean, 31 years) and measured the changes in total hemoglobin, serum albumin, and total blood water over time. The changes were expressed as fractioned dilution and then plotted against time. The curves were fitted to a one-volume and a two-volume model, which allowed an estimation of the size of the body fluid space expanded by the fluid (V) and the elimination rate constant (k(r) to be made. RESULTS: The changes in blood water concentration indicated a mean size of V of 5.9 1 (+/- 0.8, SEM) for Ringer's solution, 2.6 (+/- 0.3) 1 for dextran, and 1.2 (+/- 0.1) 1 for hypertonic saline. The corresponding values of k(r) were 94 (+/- 42), 12 (+/- 6), and 30 (+/- 4) ml/min, respectively. Blood hemoglobin indicated a degree of dilution similar to that indicated by blood water. Serum albumin indicated a more pronounced dilution, which resulted in a larger expandable volume and a greater mean square error for the curvefitting. The larger volume obtained for serum albumin can probably be explained by a loss of intravascular albumin into the tissues along with the infused fluid. CONCLUSIONS: The distribution of intravenous fluids can be analyzed by a kinetic model adapted for fluid spaces, but slightly different results are obtained, depending on the marker used to indicate dilution of the primary fluid space. Analysis and simulation of plasma volume expansion by this model is a tool that can help the anesthetist to better plan fluid therapy.

Adult↗
PubMed1989

Solitary defect on liver sulfur colloid imaging secondary to focal fatty infiltration.

Radionuclide liver-spleen imaging using Tc-99m SC may identify focal defects on routine examinations. Fatty infiltration has generally been described as a diffuse process in the liver that may be manifested on Tc-99m SC liver imaging as a nonhomogeneous pattern of radiopharmaceutical distribution or multiple small defects. This case demonstrates a focal defect on radionuclide imaging, simulating a space-occupying lesion that ultimately proved to be focal fatty infiltration. Although not an uncommon finding on CT, to the authors' knowledge this has not been reported in the nuclear medicine literature to date.

Adipose Tissue↗
PubMed1997

Diffusive transport of radon in a homogeneous column of dry sand.

To validate a model for radon transport in soil, measurements of diffusive radon transport under well-defined and controlled conditions have been made in a homogeneous column of dry sand with an air-filled volume on top. This volume simulates a crawl space. The measurements concern time-dependent diffusive transport with several different crawl-space heights and steady-state diffusive transport with different crawl-space ventilation rates. This study forms part of an extensive validation which will also cover more complex situations (e.g., advective transport, presence of pore-water). Properties of the sand that are presently being used in the radon transport model were determined from independent measurements. The comparison between model calculations and experimental results showed a good correspondence with maximum deviations of less than 10%.

Air Pollution, Indoor↗
PubMed1998

Combined diffusive and advective transport of radon in a homogeneous column of dry sand.

To validate a model for radon transport in soil, measurements of combined advective and diffusive radon transport under well-defined and controlled conditions have been made in a homogeneous column of dry sand with and without an air-filled volume on top. This volume simulates a crawl space. The measurements concern steady-state as well as time-dependent combined advective and diffusive transport and are performed in the framework of a systematic validation study which will also cover more complex situations (e.g., presence of pore-water). The experimental data were compared with results of a two-dimensional numerical model based on the finite-difference approach of the differential equation describing radon transport. Validations of the numerical model with analytical solutions were carried out for one-dimensional steady-state combined diffusive and advective transport, and for two-dimensional time-dependent diffusive transport. The results of the measurements with combined advective and diffusive transport are in good agreement with (numerical) model calculations with maximum deviations <10%.

Diffusion↗
PubMed2002

Anomalous tag diffusion in the asymmetric exclusion model with particles of arbitrary sizes.

Anomalous behavior of correlation functions of tagged particles are studied in generalizations of the one-dimensional asymmetric exclusion problem. In these generalized models the range of the hard-core interactions are changed and the restriction of relative ordering of the particles is partially broken. The models probing these effects are those of biased diffusion of particles having size S=0,1,2, em leader, or an effective negative "size" S=-1,-2, em leader, in units of lattice space. Our numerical simulations show that irrespective of the range of the hard-core potential, as long some relative ordering of particles are kept, we find suitable sliding-tag correlation functions whose fluctuations growth with time anomalously slow (t1/3), when compared with the normal diffusive behavior (t1/2). These results indicate that the critical behavior of these stochastic models are in the Kardar-Parisi-Zhang (KPZ) universality class. Moreover a previous Bethe-ansatz calculation of the dynamical critical exponent z, for size S> or =0 particles is extended to the case S<0 and the KPZ result z=3/2 is predicted for all values of S in Z.

Journal Article↗
PubMed2004

Reaction front propagation in a turbulent flow.

The propagation of reaction fronts in a turbulent fluid flow is studied by direct numerical simulations in two space dimensions. The velocity field is obtained from integrating the Navier-Stokes equation in two dimensions. We investigate the structure of the reaction front and the enhancement of the front propagation speed due to turbulent mixing. Consistently with earlier theoretical, predictions and experiments we find two qualitatively different regimes as the Damköhler number-the ratio of eddy turnover times and of the characteristic chemical time scale-is varied, corresponding to a distributed reaction zone and thin wrinkled fronts.

Journal Article↗