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At least 865 records · Page 48Linked to original sources

PubMed2003

A human model for road safety: from geometrical acquisition to model validation with radioss.

In order to investigate injury mechanisms, and to provide directions for road safety system improvements, the HUMOS project has lead to the development of a 3D finite element model of the human body in driving position. The model geometry was obtained from a 50th percentile adult male. It includes the description of all compact and trabecular bones, ligaments, tendons, skin, muscles and internal organs. Material properties were based on literature data and specific experiments performed for the project. The validation of the HUMOS model was first achieved on isolated segments and then on the whole model in both frontal and lateral impact situations. HUMOS responses were in good agreement with the experimental data used in the model validation and offers now a wide range of applications from crash simulation, optimization of safety systems, to biomedical and ergonomics.

Abdomen↗

PubMed2006

Structure of the 21-30 fragment of amyloid beta-protein.

Folding and self-assembly of the 42-residue amyloid beta-protein (Abeta) are linked to Alzheimer's disease (AD). The 21-30 region of Abeta, Abeta(21-30), is resistant to proteolysis and is believed to nucleate the folding of full-length Abeta. The conformational space accessible to the Abeta(21-30) peptide is investigated by using replica exchange molecular dynamics simulations in explicit solvent. Conformations belonging to the global free energy minimum (the "native" state) from simulation are in good agreement with reported NMR structures. These conformations possess a bend motif spanning the central residues V24-K28. This bend is stabilized by a network of hydrogen bonds involving the side chain of residue D23 and the amide hydrogens of adjacent residues G25, S26, N27, and K28, as well as by a salt bridge formed between side chains of K28 and E22. The non-native states of this peptide are compact and retain a native-like bend topology. The persistence of structure in the denatured state may account for the resistance of this peptide to protease degradation and aggregation, even at elevated temperatures.

Amyloid beta-Peptides↗

PubMed1989

Cognitive performance deficits in a simulated climb of Mount Everest: Operation Everest II.

Cognitive function at simulated altitude was investigated in a repeated-measures, within-subject study of performance by seven volunteers in a hypobaric chamber, in which atmospheric pressure was systematically lowered over a period of 40 d to finally reach a pressure equivalent to 8,845 m, the approximate height of Mount Everest. The portable cognitive test battery used, Automated Performance Test System (APTS), was specifically designed for field research under adverse environmental conditions as evidenced by compact computer design; automated test administrations, data storage, and retrieval; psychometric properties of stability and reliability; and factorial richness. Significant impairments of cognitive function were seen for three of the five tests in the battery; on two tests, grammatical reasoning and pattern comparison, every subject showed a substantial decrement. The results are discussed in terms of the impact of altitude on specific aspects of cognitive function and the importance of having sensitive and reliable instruments to monitor such effects.

Adult↗

PubMed1981

[Biomechanical simulation model of the developmental morphology of the human skull. Further observations on the model construction].

The implementation of a software simulation of a biomechanical model of the human skull, requires a high complexity construction made by a different ellipsoids and planes. At present our model is made by a facial, post-facial, occipital and palatal ellipsoids, a basal plane with a hole, walls of the nasal cavity and conic walls of the orbital cavities. Dimension of the model resemble closely an adult human skull. The physical constants given for the constituting material those of compact bone. The cavity of the model is closed except for the hole of the basal plane and for the posterior openings of the orbital cavities. The number of elements of the model is 416.

Humans↗

PubMed1996

Three-dimensional solution structure of mu-conotoxin GIIIB, a specific blocker of skeletal muscle sodium channels.

The three-dimensional solution structure of mu-conotoxin GIIIB, a 22-residue polypeptide from the venom of the piscivorous cone snail Conus geographus, has been determined using 2D 1H NMR spectroscopy. GIIIB binds with high affinity and selectivity to skeletal muscle sodium channels and is a valuable tool for characterizing both the structure and function of these channels. Structural restraints consisting of 289 interproton distances inferred from NOEs and 9 backbone and 5 side chain dihedral angle restraints from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. In addition to the 1H NMR derived information, the 13C resonances of GIIIB were assigned at natural abundance, and hydroxyproline C beta and C gamma chemical shifts were used to distinguish between the cis and trans peptide bond conformations. The final set of 20 structures had mean pairwise rms differences over the whole molecule of 1.22 A for the backbone atoms and 2.48 A for all heavy atoms. For the well-defined region encompassing residues 3-21, the corresponding values were 0.74 and 2.54 A, respectively. GIIIB adopts a compact structure consisting of a distorted 310-helix, a small beta-hairpin, a cis-hydroxyproline, and several turns. The molecule is stabilized by three disulfide bonds, two of which connect the helix and the beta-sheet, forming a structural core with similarities to the CS alpha beta motif [Cornet, B., Bonmatin, J.-M., Hetru, C., Hoffmann, J. A., Ptak, M., & Vovelle, F. (1995) Structure 3, 435-448]. This motif is common to several families of small proteins including scorpion toxins and insect defensins. Other structural features of GIIIB include the presence of eight arginine and lysine side chains that project into the solvent in a radial orientation relative to the core of the molecule. These cationic side chains form potential sites of interaction with anionic sites on sodium channels. The global fold is similar to that reported for mu-conotoxin GIIIA, and the structure of GIIIB determined in this study provides the basis for further understanding of the structure-activity relationships of the mu-conotoxins and for their binding to skeletal muscle sodium channels.

Amino Acid Sequence↗

PubMed2000

A new model for the surface arrangement of myosin molecules in tarantula thick filaments.

Three-dimensional reconstructions of the negatively stained thick filaments of tarantula muscle with a resolution of 50 A have previously suggested that the helical tracks of myosin heads are zigzagged, short diagonal ridges being connected by nearly axial links. However, surface views of lower contour levels reveal an additional J-shaped feature approximately the size and shape of a myosin head. We have modelled the surface array of myosin heads on the filaments using as a building block a model of a two-headed regulated myosin molecule in which the regulatory light chains of the two heads together form a compact head-tail junction. Four parameters defining the radius, orientation and rotation of each myosin molecule were varied. In addition, the heads were allowed independently to bend in a plane perpendicular to the coiled-coil tail at three sites, and to tilt with respect to the tail and to twist at one of these sites. After low-pass filtering, models were aligned with the reconstruction, scored by cross-correlation and refined by simulated annealing. Comparison of the geometry of the reconstruction and the distance between domains in the myosin molecule narrowed the choice of models to two main classes. A good match to the reconstruction was obtained with a model in which each ridge is formed from the motor domain of a head pointing to the bare zone together with the head-tail junction of a neighbouring molecule. The heads pointing to the Z-disc intermittently occupy the J-position. Each motor domain interacts with the essential and regulatory light chains of the neighbouring heads. A near-radial spoke in the reconstruction connecting the backbone to one end of the ridge can be identified as the start of the coiled-coil tail.

Actin Cytoskeleton↗

PubMed2005

Compact FPGA-based beamformer using oversampled 1-bit A/D converters.

A compact medical ultrasound beamformer architecture that uses oversampled 1-bit analog-to-digital (A/D) converters is presented. Sparse sample processing is used, as the echo signal for the image lines is reconstructed in 512 equidistant focal points along the line through its in-phase and quadrature components. That information is sufficient for presenting a B-mode image and creating a color flow map. The high sampling rate provides the necessary delay resolution for the focusing. The low channel data width (1-bit) makes it possible to construct a compact beamformer logic. The signal reconstruction is done using finite impulse reponse (FIR) filters, applied on selected bit sequences of the delta-sigma modulator output stream. The approach allows for a multichannel beamformer to fit in a single field programmable gate array (FPGA) device. A 32-channel beamformer is estimated to occupy 50% of the available logic resources in a commercially available mid-range FPGA, and to be able to operate at 129 MHz. Simulation of the architecture at 140 MHz provides images with a dynamic range approaching 60 dB for an excitation frequency of 3 MHz.

Analog-Digital Conversion↗

PubMed2005

Microembolic signal characterization using adaptive chirplet expansion.

The adaptive chirplet expansion (ACE) is proposed to characterize high-intensity, transient signals from circulating microemboli. The nonnegative adaptive spectrogram based on the ACE gives a compact representation of the microembolic signal (MES) in joint-time, frequency domain. The mean instantaneous power (MIP) and mean instantaneous frequency (MIF) of MES are estimated from the adaptive spectrogram. Then, several important characteristics of MES, such as embolus-to-blood ratio (EBR), half width maximum (HWM), and embolic signal onset (ESO), are computed from the MIP, and the frequency modulation is examined in the MIF. To validate the new method, we improved the simulation model of the audio Doppler ultrasound signal. Some MESs together with a Doppler ultrasound signal from carotid blood flow are simulated in the simulation study. As a comparison, the adaptive Gabor expansion (AGE) also is implemented on these simulated signals. The experimental results of the simulation study show that the new method, based on the ACE, outperforms the AGE-based method in MES characterization. The consistent conclusion has been confirmed by the clinical study on some clinical MESs.

Algorithms↗

PubMed2004

Mechanism of DNA compaction by yeast mitochondrial protein Abf2p.

We used high-resolution atomic force microscopy to image the compaction of linear and circular DNA by the yeast mitochondrial protein Abf2p, which plays a major role in packaging mitochondrial DNA. Atomic force microscopy images show that protein binding induces drastic bends in the DNA backbone for both linear and circular DNA. At a high concentration of Abf2p DNA collapses into a tight nucleoprotein complex. We quantified the compaction of linear DNA by measuring the end-to-end distance of the DNA molecule at increasing concentrations of Abf2p. We also derived a polymer statistical mechanics model that provides a quantitative description of compaction observed in our experiments. This model shows that sharp bends in the DNA backbone are often sufficient to cause DNA compaction. Comparison of our model with the experimental data showed excellent quantitative correlation and allowed us to determine binding characteristics for Abf2p. These studies indicate that Abf2p compacts DNA through a simple mechanism that involves bending of the DNA backbone. We discuss the implications of such a mechanism for mitochondrial DNA maintenance and organization.

Binding Sites↗

PubMed2004

Constructing diffeomorphic representations for the groupwise analysis of nonrigid registrations of medical images.

Groupwise nonrigid registrations of medical images define dense correspondences across a set of images, defined by a continuous deformation field that relates each target image in the group to some reference image. These registrations can be automatic, or based on the interpolation of a set of user-defined landmarks, but in both cases, quantifying the normal and abnormal structural variation across the group of imaged structures implies analysis of the set of deformation fields. We contend that the choice of representation of the deformation fields is an integral part of this analysis. This paper presents methods for constructing a general class of multi-dimensional diffeomorphic representations of deformations. We demonstrate, for the particular case of the polyharmonic clamped-plate splines, that these representations are suitable for the description of deformations of medical images in both two and three dimensions, using a set of two-dimensional annotated MRI brain slices and a set of three-dimensional segmented hippocampi with optimized correspondences. The class of diffeomorphic representations also defines a non-Euclidean metric on the space of patterns, and, for the case of compactly supported deformations, on the corresponding diffeomorphism group. In an experimental study, we show that this non-Euclidean metric is superior to the usual ad hoc Euclidean metrics in that it enables more accurate classification of legal and illegal variations.

Algorithms↗

PubMed2006

Role of protein cavities on unfolding volume change and on internal dynamics under pressure.

The effects of two single point cavity forming mutations, F110S and I7S, on the unfolding volume change (DeltaV(0)) of azurin from Pseudomonas aeruginosa and on the internal dynamics of the protein fold under pressure were probed by the fluorescence and phosphorescence emission of Trp-48, deeply buried in the compact hydrophobic core of the macromolecule. Pressure-induced unfolding, monitored by the shift of the center of mass of the fluorescence spectrum, showed that DeltaV(0) is in the range of 60-70 mL/mol, not significantly different between cavity mutants and compact azurin species such as the wild-type and the mutant C3A/C26A, in which the superficial disulphide has been removed. The lack of extra volume in F110S and I7S proves that the engineered cavities, 40 A(3) in I7S and 100 A(3) in F110S, are filled with water molecules. Changes in flexibility of the protein matrix around the chromophore were monitored by the intrinsic phosphorescence lifetime (tau(0)). The application of pressure in the predenaturation range initially decreases the internal flexibility of azurin, the trend eventually reverting on approaching unfolding. The main difference between compact folds, wild-type and C3A/C26A, and cavity mutants is that the inversion point is powered from approximately 3 kbar to 1.5 kbar for F110S and <0.1 kbar for I7S, meaning that in the latter species pressure-induced internal hydration dominates very early over any compaction of the globular fold resulting from the reduction of internal free volume. The similar response between wild-type and the significantly less-stable C3A/C26A mutant suggests that thermodynamic stability per se is not the dominant factor regulating pressure-induced internal hydration of proteins.

Azurin↗

PubMed1991

Three-dimensional structure of a complement control protein module in solution.

The complement control protein (CCP) modules (also known as short consensus repeats) are defined by a consensus sequence within a stretch of about 60 amino acid residues. These modules have been identified more than 140 times in over 20 proteins, including 12 proteins of the complement system. The solution structure of the 16th CCP module from human complement factor H has been determined by a combination of 2-dimensional nuclear magnetic resonance spectroscopy and restrained simulated annealing. In all, 548 structurally important nuclear Overhauser enhancement cross-peaks were quantified as distance restraints and, together with 41 experimentally measured angle restraints, were incorporated into a simulated annealing protocol to determine a family of closely related structures that satisfied the experimental observations. The CCP structure is shown to be based on a beta-sandwich arrangement; one face made up of three beta-strands hydrogen-bonded to form a triple-stranded region at its centre and the other face formed from two separate beta-strands. Both faces of the molecule contribute highly conserved hydrophobic side-chains to a compact core. The regions between the beta-strands are composed of both well-defined turns and less well-defined loops. Analysis of CCP sequence alignments, in light of the determined structure, reveals a high degree of conservation amongst residues of obvious structural importance, while almost all insertions, deletions or replacements observed in the known sequences are found in the less well-defined loop regions. On the basis of these observations it is postulated that models of other CCP modules that are based on the structure presented here will be accurate. Certain families of CCP modules differ from the consensus in that they contain extra cysteine residues. As a test of structural consensus, the extra disulphide bridges are shown to be easily accommodated within the determined CCP model.

Amino Acid Sequence↗

PubMed2005

Single-optical-element soft-x-ray interferometry with a laser-plasma x-ray source.

We report on a compact interferometer for the water-window soft-x-ray range that is suitable for operation with laser-plasma sources. The interferometer consists of a single diffractive optical element that focuses impinging x rays to two focal spots. The light from these two secondary sources forms the interference pattern. The interferometer was operated with a liquid-nitrogen jet laser-plasma source at lambda=2.88 nm. Scalar wave-field propagation was used to simulate the interference pattern, showing good correspondence between theoretical and experimental results. The diffractive optical element can simultaneously be used as an imaging optic, and we demonstrate soft-x-ray microscopy with interferometric contrast enhancement of a phase object.

Journal Article↗

PubMed2005

Support vector clustering for brain activation detection.

In this paper, we propose a new approach to detect activated time series in functional MRI using support vector clustering (SVC). We extract Fourier coefficients as the features of fMRI time series and cluster these features by SVC. In SVC, these features are mapped from their original feature space to a very high dimensional kernel space. By finding a compact sphere that encloses the mapped features in the kernel space, one achieves a set of cluster boundaries in the feature space. The SVC is an effective and robust fMRI activation detection method because of its advantages in (1) better discovery of real data structure since there is no cluster shape restriction, (2) high quality detection results without explicitly specifying the number of clusters, (3) the stronger robustness due to the mechanism in outlier elimination. Experimental results on simulated and real fMRI data demonstrate the effectiveness of SVC.

Algorithms↗

PubMed1997

Definition of the switch surface in the solution structure of Cdc42Hs.

Proteins of the rho subfamily of ras GTPases have been shown to be crucial components of pathways leading to cell growth and the establishment of cell polarity and mobility. Presented here is the solution structure of one such protein, Cdc42Hs, which provides insight into the structural basis for specificity of interactions between this protein and its effector and regulatory proteins. Standard heteronuclear NMR methods were used to assign the protein, and approximately 2100 distance and dihedral angle constraints were used to calculate a set of 20 structures using a combination of distance geometry and simulated annealing refinement. These structures show overall similarity to those of other GTP-binding proteins, with some exceptions. The regions corresponding to switch I and switch II in H-ras are disordered, and no evidence was found for an alpha-helix in switch II. The 13-residue insertion, which is only present in rho-subtype proteins and has been shown to be an important mediator of binding of regulatory and target proteins, forms a compact structure containing a short helix lying adjacent to the beta4-alpha3 loop. The insert forms one edge of a "switch surface" and, unexpectedly, does not change conformation upon activation of the protein by the exchange of GTP analogs for GDP. These studies indicate the insert region forms a stable invariant "footrest" for docking of regulatory and effector proteins.

Amino Acid Sequence↗

PubMed2002

In situ study of partially crystallized Bioglass and hydroxylapatite in vitro bioactivity using atomic force microscopy.

The present work investigates, in situ, the in vitro bioactivity of partially crystallized 45S5 Bioglass (BG) as a function of immersion time in a simulated body fluid (SBF) using atomic force microscopy (AFM). The results obtained for the crystallized BG were compared to those of hydroxyapatite c- and a-faces. The calcium phosphate layer grows on the crystallized 45S5 B by multiple two-dimensional nucleation and fusion of these two-dimensional islands, which is essentially the same mode as for the hydroxyapatite c-face. The surface of the crystallized 45S5 BG was almost fully covered with a dense and compact calcium phosphate layer after 24 h. The calcium phosphate formation on the crystallized BG arises from a low surface energy of the surface layer and/or an effect of the layer to lower the resistance when the growth units of calcium phosphate incorporate into the growing island. These results indicate that the crystallized 45S5 BG is suitable to be used as a filler for polymeric matrix bioactive composites, as it maintains a high bioactivity associated with a stiffer behavior (as compared to standard BG).

Biocompatible Materials↗

PubMed2006

A nonlocal continuum model for biological aggregation.

We construct a continuum model for biological aggregations in which individuals experience long-range social attraction and short-range dispersal. For the case of one spatial dimension, we study the steady states analytically and numerically. There exist strongly nonlinear states with compact support and steep edges that correspond to localized biological aggregations, or clumps. These steady-state clumps are reached through a dynamic coarsening process. In the limit of large population size, the clumps approach a constant density swarm with abrupt edges. We use energy arguments to understand the nonlinear selection of clump solutions, and to predict the internal density in the large population limit. The energy result holds in higher dimensions as well, and is demonstrated via numerical simulations in two dimensions.

Algorithms↗

PubMed2006

Dissociation of mineral and collagen orientations may differentially adapt compact bone for regional loading environments: results from acoustic velocity measurements in deer calcanei.

In limb bone diaphyses, it is hypothesized that collagen and extra-fibrillar mineral are aligned differently in relatively simple loading conditions (e.g., habitual longitudinal compression) when compared to complex or potentially deleterious strain environments (e.g., habitual shear or tension). These putative differences in collagen/mineral organization might be adaptations that enhance toughness and fatigue resistance by controlling the direction of microdamage propagation. This study examined relationships between the non-uniform strain distribution of wild deer calcanei and elastic anisotropy of cortical bone specimens in three preparations: (1) demineralized (collagen only), (2) deproteinized (mineral only), and (3) untreated. Using simulated functional loading, the following strain data were obtained from the dorsal "compression", plantar "tension", and medial and lateral ("neutral axis") cortices of one calcaneus of each of seven pairs: (1) peak strain magnitude, (2) prevalent/predominant strain mode (compression, tension, shear), and (3) principal strain orientation with respect to the bone's long axis. In the contralateral calcanei, elastic anisotropy ratios (ARs) were calculated using acoustic velocity (longitudinal and transverse) measurements from a pair of orthogonally sliced specimens (representing each of three preparation types) from each cortex. In a separate set of seven adult calcanei, predominant collagen fiber orientation (CFO) was measured using circularly polarized light (CPL) in the four cortical locations. Results showed that, in general, elastic anisotropy was significant in each region, with ARs being significantly different from isotropy (where AR=1.0). Compared to CFO, mineral orientation more strongly influenced this anisotropy, which was most notable in the plantar "tension" cortex. High correlations (r values from -0.675 to -0.734, P<0.05) were found between collagen anisotropy obtained from acoustic data when compared to the CPL data. Significant correlations of mineral and collagen anisotropy were also found between strain mode, magnitude, and orientation (all r values approximately -0.750). The habitual compression, tension, and shear (neutral axis) regions also had different collagen/mineral organizations, which may be important in accommodating the well-known disparity in the mechanical properties of bone in these loading modes.

Acoustics↗