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PubMed2006

Basic concepts in plasma accelerators.

In this article, we present the underlying physics and the present status of high gradient and high-energy plasma accelerators. With the development of compact short pulse high-brightness lasers and electron and positron beams, new areas of studies for laser/particle beam-matter interactions is opening up. A number of methods are being pursued vigorously to achieve ultra-high-acceleration gradients. These include the plasma beat wave accelerator (PBWA) mechanism which uses conventional long pulse ( approximately 100 ps) modest intensity lasers (I approximately 10(14)-10(16) W cm(-2)), the laser wakefield accelerator (LWFA) which uses the new breed of compact high-brightness lasers (<1 ps) and intensities >10(18) W cm(-2), self-modulated laser wakefield accelerator (SMLWFA) concept which combines elements of stimulated Raman forward scattering (SRFS) and electron acceleration by nonlinear plasma waves excited by relativistic electron and positron bunches the plasma wakefield accelerator. In the ultra-high intensity regime, laser/particle beam-plasma interactions are highly nonlinear and relativistic, leading to new phenomenon such as the plasma wakefield excitation for particle acceleration, relativistic self-focusing and guiding of laser beams, high-harmonic generation, acceleration of electrons, positrons, protons and photons. Fields greater than 1 GV cm(-1) have been generated with monoenergetic particle beams accelerated to about 100 MeV in millimetre distances recorded. Plasma wakefields driven by both electron and positron beams at the Stanford linear accelerator centre (SLAC) facility have accelerated the tail of the beams.

Computer Simulation↗
PubMed1998

Anesthesia control using midlatency auditory evoked potentials.

This paper shows the development of a system to control inhalation anesthetic concentration delivered to a patient based upon that patient's midlatency auditory evoked potentials (MLAEP's). It was developed and tested in dogs by determining response to the supramaximal stimulus of tail clamping. Prior to tail clamp, the MLAEP was recorded along with inhalational anesthetic concentration and classified as responders or nonresponders as determined by tail clamping. This was performed at a number of different anesthetic levels to obtain a data training set. The MLAEP's were compacted by means of discrete time wavelet transform (DTWT), and together with anesthetic concentration value, a stepwise discriminant analysis (SDA) was performed to determine those features which could separate responders from nonresponders. It was determined that only three features were necessary for this recognition. These features were then used to train a four-layer artificial neural network (ANN) to separate the responders from nonresponders. The network was tested using a separate set of data, resulting in a 93% recognition rate in the anesthetic transition zone between responders and nonresponders, and 100% recognition rate outside this zone. The anesthetic controller used this ANN combined with fuzzy logic and rule-based control. A set of ten animal experiments were performed to test the robustness of this controller. Acceptable clinical performance was obtained, showing the feasibility of this approach.

Anesthesia↗
PubMed2005

Diffuse boundary extraction of breast masses on ultrasound by leak plugging.

We propose a semiautomated seeded boundary extraction algorithm that delineates diffuse region boundaries by finding and plugging their leaks. The algorithm not only extracts boundaries that are partially diffuse, but in the process finds and quantifies those parts of the boundary that are diffuse, computing local sharpness measurements for possible use in computer-aided diagnosis. The method treats a manually drawn seed region as a wellspring of pixel "fluid" that flows from the seed out towards the boundary. At indistinct or porous sections of the boundary, the growing region will leak into surrounding tissue. By changing the size of structuring elements used for growing, the algorithm changes leak properties. Since larger elements cannot leak as far from the seed, they produce compact, less detailed boundary approximations; conversely, growing from smaller elements results in less constrained boundaries with more local detail. This implementation of the leak plugging algorithm decrements the radius of structuring disks and then compares the regions grown from them as they increase in both area and boundary detail. Leaks are identified if the outflows between grown regions are large compared to the areas of the disks. The boundary is plugged by masking out leaked pixels, and the process continues until one-pixel-radius resolution. When tested against manual delineation on scans of 40 benign masses and 40 malignant tumors, the plugged boundaries overlapped and correlated well in area with manual tracings, with mean overlap of 0.69 and area correlation R2 of 0.86, but the algorithm's results were more reproducible.

Algorithms↗
PubMed1994

[Numerical treatment of bone as anisotropic material].

A three-dimensional finite element model of the femur shaft taking account of its microscopic structure has been developed. In the first instance, the material properties of a homogenised material replacing the inhomogeneous structure of compact bone were determined with the aid of a two-dimensional finite element model containing information on the bone structure and the mechanical behaviour of osteons. The bone structure with its irregular hole pattern (Haversian canals of the osteons) was idealised by assuming the bone to be a homogeneous plate with the holes arranged in a hexagonal or square pattern. The regular structure considered allowed on to compute the stresses and deformations of a modelled characteristic segment under given boundary conditions and loads. With these values new material constants (Young's and shear moduli, Poisson's ratios) of the continuum substitute were calculated. These constants were the material properties of the three-dimensional finite element model of the femur shaft, which was then used for stress calculations under the load components of the one-legged stance.

Anisotropy↗
PubMed1998

Conformational analysis of the endogenous mu-opioid agonist endomorphin-1 using NMR spectroscopy and molecular modeling.

Endomorphin-1 (Tyr-Pro-Trp-Phe-NH2) is a highly selective and potent agonist of the mu-opioid receptor. To identify structural attributes unique to this opioid peptide and potential sites of recognition, a conformational analysis has been performed using multidimensional NMR and molecular modeling techniques. The spectroscopic results, derived from experiments in both DMSO and water, indicate that endomorphin-1 exists in the cis- and trans-configuration with respect to the Pro-omega bond in approximately 25% and 75% populations, respectively. In DMSO, the cis-configuration adopts a compact sandwich conformation in which the Tyr and Trp aromatic rings pack against the proline ring, whereas the trans-configuration adopts an extended conformation. Although non-random structure was not observed in water, condensed phase molecular dynamics calculations indicate that trans-isomers dominate the population in this higher dielectric medium. Structural comparison of the cis- and trans-configurations with morphine and selective mu-peptide ligands PL-017 and D-TIPP, as well as the delta-selective peptide ligands TIPP (delta-antagonist, mu-agonist) and DPDPE were also performed and suggest the trans-isomer is likely the bioactive form. A hypothesis is proposed to explain mu- and delta-selectivity based on the presence of spatially distinct selectivity pockets among these ligands.

Computer Simulation↗
PubMed2006

Design and calibration of a compact multi-frequency EIT system for acute stroke imaging.

A new, compact UCLH Mk 2.5 EIT system has been developed and calibrated for EIT imaging of the head. Improvements include increased input and output impedances, increased bandwidth and improved CMRR (80 dB) and linearity over frequencies and load (0.2% on a single channel, +/-0.7% on a saline tank over 20 Hz-256 kHz and 10-65 Omega). The accuracy of the system is sufficient to image severe acute stroke according to the specification from recent detailed anatomical modelling (Horesh et al 2005 3rd European Medical and Biological Engineering Conference EMBEC'05). A preliminary human study has validated the main specifications of the modelling, the range of trans-impedance from the head (8-70 Omega) using a 32 electrode, 258 combination protocol and contact impedances of 300 Omega to 2.7 kOmega over 20 Hz to 256 kHz.

Acute Disease↗
PubMed2005

'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.

MOTIVATION: The object of this study is to propose a new method to identify small compact units that compose protein three-dimensional structures. These fragments, called 'protein units (PU)', are a new level of description to well understand and analyze the organization of protein structures. The method only works from the contact probability matrix, i.e. the inter Calpha-distances translated into probabilities. It uses the principle of conventional hierarchical clustering, leading to a series of nested partitions of the 3D structure. Every step aims at dividing optimally a unit into 2 or 3 subunits according to a criterion called 'partition index' assessing the structural independence of the subunits newly defined. Moreover, an entropy-derived squared correlation R is used for assessing globally the protein structure dissection. The method is compared to other splitting algorithms and shows relevant performance. AVAILABILITY: An Internet server with dedicated tools is available at http://www.ebgm.jussieu.fr/~gelly/

Algorithms↗
PubMed2006

Condensation of DNA-actin polyelectrolyte mixtures driven by ions of different valences.

Multivalent ions can induce condensation of like-charged polyelectrolytes into compact states, a process that requires different ion valences for different polyelectrolyte species. In this work we examine the condensation behavior in binary anionic polyelectrolyte mixtures consisting of DNA coils and F-actin rods in the presence of monovalent, divalent, and trivalent ions. As expected, monovalent ions do not condense either component and divalent ions selectively condense F-actin rods out of the polyelectrolyte mixture. For trivalent ions, however, we observe a microphase separation between the two polyelectrolytes into coexisting finite-sized F-actin bundles and DNA toroids. Further, by increasing the DNA volume fraction in the mixture, condensed F-actin bundles can be completely destabilized, leading to only DNA condensation within the mixture. We examine a number of possible causes and propose a model based on polyelectrolyte competition for ions.

Actins↗
PubMed2003

Conformational dynamics of partially denatured myoglobin studied by time-resolved electrospray mass spectrometry with online hydrogen-deuterium exchange.

This study demonstrates the use of electrospray mass spectrometry in conjunction with rapid online mixing ("time-resolved" ESI-MS) for monitoring protein conformational dynamics under equilibrium conditions. The hydrogen/deuterium exchange (HDX) kinetics of mildly denatured myoglobin (Mb) at pD 9.3, in the presence of 27% acetonitrile, were studied with millisecond time resolution. Analytical ultracentrifugation indicates that the average protein compactness under these solvent conditions is similar to that of native holomyoglobin (hMb). The mass spectrum shows protein ions in a wide array of charge and heme binding states, indicating the presence of multiple coexisting conformations. The experimental approach used allows the HDX kinetics of all of these species to be monitored separately. A combination of EX1 and EX2 behavior was observed for hMb ions in charge states 7+ to 9+, which predominantly represent nativelike hMb in solution. The EX1 kinetics are biphasic, indicating the presence of two protein populations that undergo conformational opening events with different rate constants. The EX2 kinetics observed for nativelike hMb are biphasic as well. All other charge and heme binding states represent non-native protein conformations that are involved in rapid interconversion processes, thus leading to monoexponential EX2 kinetics with a common rate constant. Burst phase labeling for these non-native proteins occurs at 125 sites. In contrast, the nativelike protein conformation shows burst phase labeling only for 88 sites. A kinetic model is developed which is based on the assumption of three distinct (un)folding units in Mb. The model implies that the free energy landscape of the protein exhibits a major barrier. The crossing of this barrier is most likely associated with slow, cooperative opening/closing events of the heme binding pocket. Rapid conformational fluctuations on either side of the barrier give rise to the observed EX2 kinetics. Simulated HDX kinetics based on this model are in excellent agreement with the experimental data.

Animals↗
PubMed2004

Genome image programs: visualization and interpretation of Escherichia coli microarray experiments.

We have developed programs to facilitate analysis of microarray data in Escherichia coli. They fall into two categories: manipulation of microarray images and identification of known biological relationships among lists of genes. A program in the first category arranges spots from glass-slide DNA microarrays according to their position in the E. coli genome and displays them compactly in genome order. The resulting genome image is presented in a web browser with an image map that allows the user to identify genes in the reordered image. Another program in the first category aligns genome images from two or more experiments. These images assist in visualizing regions of the genome with common transcriptional control. Such regions include multigene operons and clusters of operons, which are easily identified as strings of adjacent, similarly colored spots. The images are also useful for assessing the overall quality of experiments. The second category of programs includes a database and a number of tools for displaying biological information about many E. coli genes simultaneously rather than one gene at a time, which facilitates identifying relationships among them. These programs have accelerated and enhanced our interpretation of results from E. coli DNA microarray experiments. Examples are given.

Chromosome Mapping↗
PubMed1995

Impact of local and non-local interactions on thermodynamics and kinetics of protein folding.

To address the question of how the geometry of a protein's native conformation affects its folding and stability, we studied three model 36-mers on a cubic lattice. The native structure of one of these model 36-mers consisted mostly of local contacts, while that of a second consisted mostly of non-local contacts. The third native structure had a typical compact native conformation, and served as our reference. For each protein, the amino acid sequence was designed to have a pronounced energy minimum at its native conformation. We observed dramatic differences in folding, dependent on the presence or absence of non-local contacts. For the proteins with a typical large number of non-local contacts, the folding transition was all-or-none, whereas for the one with mostly local contacts, it was not. Although the maximum rate of folding was similar for all three proteins, we found that under conditions at which each native conformation was stable, the structure with mostly non-local contacts folded two orders of magnitude faster than the one with mostly local contacts. The statistical analysis of protein structure agrees fully with the implications of the theory. We discuss the importance of cooperativity in protein folding for its stability.

Amino Acid Sequence↗
PubMed2004

Adenylation-dependent conformation and unfolding pathways of the NAD+-dependent DNA ligase from the thermophile Thermus scotoductus.

In the last few years, an increased attention has been focused on NAD(+)-dependent DNA ligases. This is mostly due to their potential use as antibiotic targets, because effective inhibition of these essential enzymes would result in the death of the bacterium. However, development of an efficient drug requires that the conformational modifications involved in the catalysis of NAD(+)-dependent DNA ligases are understood. From this perspective, we have investigated the conformational changes occurring in the thermophilic Thermus scotoductus NAD(+)-DNA ligase upon adenylation, as well as the effect of cofactor binding on protein resistance to thermal and chemical (guanidine hydrochloride) denaturation. Our results indicate that cofactor binding induces conformational rearrangement within the active site and promotes a compaction of the enzyme. These data support an induced "open-closure" process upon adenylation, leading to the formation of the catalytically active enzyme that is able to bind DNA. These conformational changes are likely to be associated with the protein function, preventing the formation of nonproductive complexes between deadenylated ligases and DNA. In addition, enzyme adenylation significantly increases resistance of the protein to thermal denaturation and GdmCl-induced unfolding, establishing a thermodynamic link between ligand binding and increased conformational stability. Finally, chemical unfolding of deadenylated and adenylated enzyme is accompanied by accumulation of at least two equilibrium intermediates, the molten globule and premolten globule states. Maximal populations of these intermediates are shifted toward higher GdmCl concentrations in the case of the adenylated ligase. These data provide further insights into the properties of partially folded intermediates.

Adenine↗
PubMed2005

A hip wear simulator with 100 test stations.

A novel high-capacity hip wear simulator of the pin-on-disc type was designed, built, and validated. This so-called Super-CTPOD (circularly translating pin-on-disc) device has as many as 100 separate test stations, being an advanced version of the previously validated 12-station CTPOD. A validity test was done so that in all stations the specimens and the test conditions were as similar as possible. Hence, for the first time in this field, an adequate number of similar tests was done for a proper statistical analysis of wear data. The pins were conventional, gamma-sterilized ultra-high molecular weight polyethylene, and the discs were polished CoCr. The lubricant was diluted calf serum and the test length 3 million cycles. In the course of the test, the pins became highly polished, whereas the discs remained practically unchanged. The majority of the polyethylene wear particles were rounded, with a mean diameter of 0.25 microm. The 100 wear factor values computed from the 100 steady state wear rate values of the pins were normally distributed, the mean +/- 95 per cent confidence interval being 1.63 +/- 0.017 x 10(-6) mm3 /N m. The standard deviation was 5.4 per cent of the mean. There were no outliers. The wear mechanisms and the wear factor agreed well with clinical findings. Altogether, the Super-CTPOD test system was shown to be a unique combination of validity, low variation, capacity, efficiency, reliability, productivity, economy, ease of operation, and compact size.

Equipment Design↗
PubMed2006

Protein disorder prediction by condensed PSSM considering propensity for order or disorder.

BACKGROUND: More and more disordered regions have been discovered in protein sequences, and many of them are found to be functionally significant. Previous studies reveal that disordered regions of a protein can be predicted by its primary structure, the amino acid sequence. One observation that has been widely accepted is that ordered regions usually have compositional bias toward hydrophobic amino acids, and disordered regions are toward charged amino acids. Recent studies further show that employing evolutionary information such as position specific scoring matrices (PSSMs) improves the prediction accuracy of protein disorder. As more and more machine learning techniques have been introduced to protein disorder detection, extracting more useful features with biological insights attracts more attention. RESULTS: This paper first studies the effect of a condensed position specific scoring matrix with respect to physicochemical properties (PSSMP) on the prediction accuracy, where the PSSMP is derived by merging several amino acid columns of a PSSM belonging to a certain property into a single column. Next, we decompose each conventional physicochemical property of amino acids into two disjoint groups which have a propensity for order and disorder respectively, and show by experiments that some of the new properties perform better than their parent properties in predicting protein disorder. In order to get an effective and compact feature set on this problem, we propose a hybrid feature selection method that inherits the efficiency of uni-variant analysis and the effectiveness of the stepwise feature selection that explores combinations of multiple features. The experimental results show that the selected feature set improves the performance of a classifier built with Radial Basis Function Networks (RBFN) in comparison with the feature set constructed with PSSMs or PSSMPs that adopt simply the conventional physicochemical properties. CONCLUSION: Distinguishing disordered regions from ordered regions in protein sequences facilitates the exploration of protein structures and functions. Results based on independent testing data reveal that the proposed predicting model DisPSSMP performs the best among several of the existing packages doing similar tasks, without either under-predicting or over-predicting the disordered regions. Furthermore, the selected properties are demonstrated to be useful in finding discriminating patterns for order/disorder classification.

Amino Acid Sequence↗
PubMed2004

Kinetics and thermodynamics of the unfolding and refolding of the three-stranded alpha-helical coiled coil, Lpp-56.

Temperature-induced reversible unfolding and refolding of the three-stranded alpha-helical coiled coil, Lpp-56, were studied by kinetic and thermodynamic methods, using CD spectroscopy, dynamic light scattering, and scanning calorimetry. It was found that both unfolding and refolding reactions of this protein in neutral solution in the presence of 100 mM NaCl are characterized by unusually slow kinetics, which permits detailed investigation of the mechanism of these reactions. Kinetic analyses show that the unfolding of this coiled coil represents a single-stage first-order reaction, while the refolding represents a single-stage third-order reaction. The activation enthalpy and entropy for unfolding do not depend noticeably on temperature and are both significantly greater than those for the folding reaction, which show a significant dependence on temperature. The activation heat capacity change for the unfolding reaction is close to zero, while it is quite significant for the folding reaction. The correlation between the activation and structural parameters obtained for the Lpp-56 coiled coil suggests that interhelical van der Waals interactions are disrupted in the transition state, which is nevertheless still compact, and water has not yet penetrated into the interface; the transition from the transient state to the unfolded state results in hydration of exposed apolar groups of the interface and the disruption of helices. The low propensity for the Lpp-56 strands to fold and associate is caused by the high number of charged groups at neutral pH. On one hand, these charges give rise to considerable repulsive forces destabilizing the helical conformation of the strands. On the other hand, they align the folded helices in parallel and in register so that the apolar sides face each other, and the oppositely charged groups may form salt links, which are important for the formation of the trimeric coiled coil. A decrease in pH, which eliminates the salt links, dramatically decreases the stability of Lpp-56; its structure becomes less rigid and unfolds much faster.

Amino Acid Sequence↗
PubMed2004

Structure of the C-terminal domain from Trypanosoma brucei variant surface glycoprotein MITat1.2.

The variant surface glycoprotein (VSG) of African trypanosomes has a structural role in protecting other cell surface proteins from effector molecules of the mammalian immune system and also undergoes antigenic variation necessary for a persistent infection in a host. Here we have reported the solution structure of a VSG type 2 C-terminal domain from MITat1.2, completing the first structure of both domains of a VSG. The isolated C-terminal domain is a monomer in solution and forms a novel fold, which commences with a short alpha-helix followed by a single turn of 3(10)-helix and connected by a short loop to a small anti-parallel beta-sheet and then a longer alpha-helix at the C terminus. This compact domain is flanked by two unstructured regions. The structured part of the domain contains 42 residues, and the core comprises 2 disulfide bonds and 2 hydrophobic residues. These cysteines and hydrophobic residues are conserved in other VSGs, and we have modeled the structures of two further VSG C-terminal domains using the structure of MITat1.2. The models suggest that the overall structure of the core is conserved in the different VSGs but that the C-terminal alpha-helix is of variable length and depends on the presence of charged residues. The results provided evidence for a conserved tertiary structure for all the type 2 VSG C-terminal domains, indicated that VSG dimers form through interactions between N-terminal domains, and showed that the selection pressure for sequence variation within a conserved tertiary structure acts on the whole of the VSG molecule.

Amino Acid Sequence↗
PubMed2004

A three-dimensional kinematic and dynamic study of the lower limb during the stance phase of gait using an homogeneous matrix approach.

This paper presents a method to analyze three dimensional kinematics and dynamics of lower limb during walking. The proposed method is based on a homogeneous matrix concept, derived from robotics and using compact, expressive notation convenient for computer applications. The major advantage of this method is that no hypothesis is required on the joint model, which makes it applicable to complex and pathologic joints. Kinematic data are computed from 3-D trajectories of markers collected by a motion analysis system. External forces applied on the leg are measured synchronously during the stance phase of gait. Angular velocity components obtained using the homogeneous matrix method are displayed for three subjects and compared with those obtained from the same experimental data using a helical axis method. Then, intersegmental moments calculated from the inverse dynamic part of the homogeneous matrix method are shown on the same subjects. Kinematic results indicate that there are no significant differences between the methods, thus demonstrating the reproducibility of the stance phase of gait in the sagittal plane. Use of this synthetic homogeneous method developed for both kinematics and dynamics of rigid bodies demonstrates good promise for applications in biomechanics.

Adult↗
PubMed2004

Interactions of the neurotoxin vipoxin in solution studied by dynamic light scattering.

The neurotoxin vipoxin is the lethal component of the venom of Vipera ammodytes meridionalis. It is a heterodimer of a basic toxic His-48 phospholipase A2 (PLA2) and an acidic nontoxic Gln-48 PLA2. The shape of the neurotoxin and its separated components in solution as well as their interactions with calcium, the brain phospholipid phosphatidylcholine, and two inhibitors, elaidoylamide and vitamin E, were investigated by dynamic light scattering. Calcium binding is connected with a conformational change in vipoxin observed as a change of the hydrodynamic shape from oblate ellipsoid to a shape closer to a sphere. The Ca2+-bound form of vipoxin, which is catalytically active, is more compact and symmetric than the calcium-free heterodimer. Similar changes were observed as a result of the Ca2+-binding to the two separated subunits. In the presence of aggregated phosphatidylcholine, the neurotoxic complex dissociates to subunits. It is supposed that only the toxic component binds to the substrate, and the other subunit, which plays a chaperone function, remains in solution. The inhibition of vipoxin with the synthetic inhibitor elaidoylamide and the natural compound vitamin E changes the shape of the toxin from oblate to prolate ellipsoid. The inhibited toxin is more asymmetric in comparison to the native one. Similar, but not so pronounced, effects were observed after the inhibition of the monomeric and homodimeric forms of the toxic His-48 PLA2. Circular dichroism measurements in the presence of urea, methylurea, and ethylurea indicate a strong hydrophobic stabilization of the neurotoxin. Hydrophobic interactions stabilize not only the folded regions but also the regions of intersubunit contacts.

Binding Sites↗