PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Compaction simulator”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 793 records · Page 44Linked to original sources
PubMed2005

Closed orbit change induced by nonzero dispersion rf cavities.

The particle motion in storage rings is coupled between the longitudinal and the transverse planes in the presence of nonzero dispersion rf cavities. We found that the particle motion can be modeled separately with a redefined closed orbit. The closed orbit can be described by a Green's function, which was confirmed in the simulation and in the experiment. The pathlength is calculated from the redefined closed orbit, and we found that the longitudinal phase slip is related not only to the momentum, but also to the rf phase of the particle. The effect on the longitudinal motion becomes significant if the phase slip caused by the rf cavities is large or if the momentum compaction factor is small, such as in the lower alpha- lattice which is intended to produce shorter bunches.

Journal Article↗
PubMed2005

Signal-dependent wavelets for electromyogram classification.

In the study, an efficient method to perform supervised classification of surface electromyogram (EMG) signals is proposed. The method is based on the choice of a relevant representation space and its optimisation with respect to a training set. As EMG signals are the summation of compact-support waveforms (the motor unit action potentials), a natural tool for their representation is the discrete dyadic wavelet transform. The feature space was thus built from the marginals of a discrete wavelet decomposition. The mother wavelet was designed to minimise the probability of classification error estimated on the learning set (supervised classification). As a representative example, the method was applied to simulate surface EMG signals generated by motor units with different degrees of short-term synchronisation. The proposed approach was able to distinguish surface EMG signals with degrees of synchronisation that differed by 10%, with a misclassification rate of 8%. The performance of a spectral-based classification (error rate approximately 33%) and of the classification with Daubechies wavelet (21%) was significantly poorer than with the proposed wavelet optimisation. The method can be used for a number of different application fields of surface EMG classification, as the feature space is adapted to the characteristics of the signal that discriminate between classes.

Action Potentials↗
PubMed2004

Mitochondrial aggregation patterns and activity in porcine oocytes and apoptosis in surrounding cumulus cells depends on the stage of pre-ovulatory maturation.

In this study, we evaluated the distribution and oxidative activity of mitochondria in ex vivo pre-ovulatory porcine oocytes using the fluorescence probe MitoTracker CMTM Ros Orange. Cumulus-oocyte complexes (COCs) were classified according to cumulus morphology and time from hCG administration. The meiotic configuration of the oocytes and the degree of apoptosis in the surrounding cumulus cells were also evaluated. Estrus was synchronized in 45 crossbred Landrace gilts by feeding altrenogest for 15 days and administering 1000 IU PMSG on Day 16. The LH peak was simulated by treatment with 500 IU hCG, given 80 h after PMSG. Endoscopic oocyte recovery was carried out 2 h before or 10, 22, or 34 h after hCG administration. Altogether 454 COCs were aspirated from follicles with a diameter of more than 5 mm. Cumulus morphology in the majority of COCs recovered 2 h before and 10 h after hCG was compact (60.4 and 52.7%, respectively; P<0.05). At 22 h after hCG, COC morphology changed significantly from 10 h dramatically: 74% of COCs had an expanded cumulus (P<0.01). At 34 h after hCG, 100% of recovered COCs had an expanded cumulus. The percentage of oocytes with a mature meiotic configuration differed among COC morphologies and increased as the interval after hCG administration increased (P<0.05). The type of mitochondrial distribution in the oocytes (n=336) changed from homogeneous to heterogeneous as the interval after hCG administration increased (P<0.01) and was associated with the cumulus morphology. Representative mitochondrial distributions were found as follows: -2 h: fine homogeneous in compact and dispersed COCs; 10 h: granulated homogeneous in compact and dispersed COCs; 22 h: granulated homogeneous in expanded COCs; and 34 h: granulated heterogeneous and clustered heterogeneous in expanded COCs (P<0.01). The oxidative activity of mitochondria measured by fluorescence intensity (Em: 570 nm) per oocyte after Mitotracker CMTM Ros Orange labeling increased in the oocyte as the post-hCG interval increased (P<0.01) and depended on the type of mitochondrial distribution. Lowest oxidative activity of mitochondria was found in oocytes with fine homogeneous distribution (253.1+/-9.4 microA). The oxidative activity increased (334.4+/-10.3 microA) in oocytes with granulated homogeneous distribution of mitochondria, and reached highest level in oocytes with granulated heterogeneous (400.9+/-13.0 microA) and clustered heterogeneous distributions (492.8+/-13.9 microA) (P<0.01). Mitochondrial activity in oocytes coincided with apoptosis in surrounding cumulus cells which increased in a time-dependent manner during pre-ovulatory maturation in vivo (P<0.01). These results indicate that there is a relationship between meiotic progression, cumulus expansion and mitochondrial redistribution and their oxidative activity during final pre-ovulatory maturation in pig oocytes. It appears that increased levels of mitochondrial activities in oocytes are correlated to increased levels of apoptosis in surrounding cumulus cells, in which mitochondria may play a role.

Animals↗
PubMed2002

Structure and properties of the dendron-encapsulated polyoxometalate (C(52)H(60)NO(12))(12)[(Mn(H(2)O))(3)(SbW(9)O(33))(2)], a first generation dendrizyme.

Combining analytical and theoretical methods, we present a detailed study of a heteropolytungstate cluster encapsulated in a shell of dendritically branching surfactants, namely (C(52)H(60)NO(12))(12)[(Mn(H(2)O))(3)(SbW(9)O(33))(2)], 3. This novel surfactant-encapsulated cluster (SEC) self-assembles spontaneously from polyoxometalate-containing solutions treated with a stoichiometric amount of dendrons. Compound 3 exhibits a discrete supramolecular architecture in which a single polyoxometalate anion resides in a compact shell of dendrons. Our approach attempts to combine the catalytic activity of polyoxometalates with the steric properties of tailored dendritic surfactants into size-selective catalytic systems. The structural characterization of the SEC is based on analytical ultracentrifugation (AUC) and small-angle neutron scattering (SANS). The packing arrangement of dendrons at the cluster surface is gleaned from molecular dynamics (MD) simulations, which suggests a highly porous shell structure due to the dynamic formation of internal clefts and cavities. From analysis of the MD trajectory of 3, a theoretical neutron-scattering function is derived that is in good agreement with experimental SANS data. Force field parameters used in MD simulations are partially derived from a quantum mechanical geometry optimization of [(Zn(H(2)O))(3)(SbW(9)O(33))(2)](12)(-), 2b, at the density functional theory (DFT) level. DFT calculations are corroborated by X-ray structure analysis of Na(6)K(6)[(Zn(H(2)O))(3)(SbW(9)O(33))(2)].23H(2)O, which is isostructural with the catalytically active Mn derivative 2a. The combined use of theoretical and analytical methods aims at rapidly prototyping smart catalysts ("dendrizymes"), which are structurally related to naturally occurring metalloproteins.

Journal Article↗
PubMed2002

Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing.

Upon cooling, water freezes to ice. This familiar phase transition occurs widely in nature, yet unlike the freezing of simple liquids, it has never been successfully simulated on a computer. The difficulty lies with the fact that hydrogen bonding between individual water molecules yields a disordered three-dimensional hydrogen-bond network whose rugged and complex global potential energy surface permits a large number of possible network configurations. As a result, it is very challenging to reproduce the freezing of 'real' water into a solid with a unique crystalline structure. For systems with a limited number of possible disordered hydrogen-bond network structures, such as confined water, it is relatively easy to locate a pathway from a liquid state to a crystalline structure. For pure and spatially unconfined water, however, molecular dynamics simulations of freezing are severely hampered by the large number of possible network configurations that exist. Here we present a molecular dynamics trajectory that captures the molecular processes involved in the freezing of pure water. We find that ice nucleation occurs once a sufficient number of relatively long-lived hydrogen bonds develop spontaneously at the same location to form a fairly compact initial nucleus. The initial nucleus then slowly changes shape and size until it reaches a stage that allows rapid expansion, resulting in crystallization of the entire system.

Journal Article↗
PubMed2003

Relevance of structural segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model.

The relevance of inside-outside segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model is probed by complete enumeration of two-dimensional chains of up to 18 monomers in the square lattice. The exact computation of Z scores for uniquely designed sequences confirms that Z tends to decrease linearly with sigma square root of N, as previously suggested by theoretical analysis and Monte Carlo simulations, where sigma, the standard deviation of the number of contacts made by different monomers in the target structure, is a measure of structural segregation and N is the chain length. The probability that the target conformation is indeed the unique global energy minimum of the designed sequence is found to increase dramatically with sigma, approaching unity at maximal segregation. However, due to the huge number of conformations with sub-maximal values of sigma, which correspond to intermediate, only mildly discriminative, values of Z, in addition to significant oscillations of Z around its estimated value, the probability that a correctly designed sequence corresponds to a maximally segregated conformation is small. This behavior of Z also explains the observed relation between sigma and different measures of folding cooperativity of correctly designed sequences.

Models, Statistical↗
PubMed1983

Capsule filling studies using an mG2 production machine.

A production mG2 G36 machine has been employed to study the effects of compression on the capsule filling properties of four particle size fractions of lactose having a range of flow properties. The effect of the surface texture of the dosator nozzle bore on capsule filling is also investigated. Fine, cohesive powders gave uniform fill weights over a whole range of compression settings but as increasingly free-flowing powders were used, this range diminishes. For both types of powder, the upper limit on compression is set by compaction of powder which produces poor fill weights; coarse, free-flowing powders, which are less compressible, compact at lower compressions. Free-flowing powders, in particular, also require a minimum compression to be retained. Resurfaced nozzles produced improved capsule filling. One nozzle surface produced slightly more uniform fill weights and was unaffected by powder coating of the nozzle suggesting that an optimum surface texture exists for capsule filling. The results are similar to those obtained using the mG2 simulator and hence validate the latter's use in studying production capsule filling.

Capsules↗
PubMed2000

Minimizing binding errors using learned conjunctive features.

We have studied some of the design trade-offs governing visual representations based on spatially invariant conjunctive feature detectors, with an emphasis on the susceptibility of such systems to false-positive recognition errors-Malsburg's classical binding problem. We begin by deriving an analytical model that makes explicit how recognition performance is affected by the number of objects that must be distinguished, the number of features included in the representation, the complexity of individual objects, and the clutter load, that is, the amount of visual material in the field of view in which multiple objects must be simultaneously recognized, independent of pose, and without explicit segmentation. Using the domain of text to model object recognition in cluttered scenes, we show that with corrections for the nonuniform probability and nonindependence of text features, the analytical model achieves good fits to measured recognition rates in simulations involving a wide range of clutter loads, word size, and feature counts. We then introduce a greedy algorithm for feature learning, derived from the analytical model, which grows a representation by choosing those conjunctive features that are most likely to distinguish objects from the cluttered backgrounds in which they are embedded. We show that the representations produced by this algorithm are compact, decorrelated, and heavily weighted toward features of low conjunctive order. Our results provide a more quantitative basis for understanding when spatially invariant conjunctive features can support unambiguous perception in multiobject scenes, and lead to several insights regarding the properties of visual representations optimized for specific recognition tasks.

Artificial Intelligence↗
PubMed2000

Minimizing binding errors using learned conjunctive features.

We have studied some of the design trade-offs governing visual representations based on spatially invariant conjunctive feature detectors, with an emphasis on the susceptibility of such systems to false-positive recognition errors-Malsburg's classical binding problem. We begin by deriving an analytical model that makes explicit how recognition performance is affected by the number of objects that must be distinguished, the number of features included in the representation, the complexity of individual objects, and the clutter load, that is, the amount of visual material in the field of view in which multiple objects must be simultaneously recognized, independent of pose, and without explicit segmentation. Using the domain of text to model object recognition in cluttered scenes, we show that with corrections for the nonuniform probability and nonindependence of text features, the analytical model achieves good fits to measured recognition rates in simulations involving a wide range of clutter loads, word size, and feature counts. We then introduce a greedy algorithm for feature learning, derived from the analytical model, which grows a representation by choosing those conjunctive features that are most likely to distinguish objects from the cluttered backgrounds in which they are embedded. We show that the representations produced by this algorithm are compact, decorrelated, and heavily weighted toward features of low conjunctive order. Our results provide a more quantitative basis for understanding when spatially invariant conjunctive features can support unambiguous perception in multiobject scenes, and lead to several insights regarding the properties of visual representations optimized for specific recognition tasks.

Algorithms↗
PubMed2003

Release of indomethacin from bioadhesive tablets containing carbopol 941 modified with Abelmuschus esculentus (okra) gum.

Carbopol 941 (C-941) and Abelmuschus esculentus gum (Okra gum, AEG) were used as bioadhesive polymers in the formulation of mucoadhesive indomethacin tablets. Different batches of the tablet compacts were formulated based on different combination ratios of the polymers. The bioadhesive properties of the tablets were studied using a tensiometer: Tablets coated with 50% w/v solution of Eudragit I. 100 in ethanol, were also prepared and evaluated. The following tablet physical properties were evaluated: hardness, uniformity of weight, disintegration time, friability, and absolute drug content. Release studies were determined in simulated intestinal fluid (SIF pH 7.2) without pancreatin, and in 0.1 N solution of HCl. Result obtained indicated that tablets with equal ratio of C-941 and AEG (1:1) gave the highest bioadhesive strength for both the coated and uncoated tablets. The percentage of drug released ranged from 53-90% for uncoated tablets in 0.1 N HCl and SIF, and 9-16% for coated tablets in 0.1 N HCl, and 63-100% for coated tablets in SIF after 8 hrs.

Abelmoschus↗
PubMed1994

Distinct structural elements and internal entry of ribosomes in mRNA3 encoded by infectious bronchitis virus.

Infectious bronchitis virus (IBV) mRNA3 encodes three small proteins, 3a, 3b, and 3c, at its 5' end. Recently, it was demonstrated that initiation of protein 3c is dependent on the upstream sequence. Monte Carlo simulations of RNA folding in this tricistronic mRNA3 indicate that a highly significant folding region occurs prior to the initiator AUG of 3c. The unusual folding region (UFR) of 265 nucleotides (nt) contains the coding sequences of proteins 3a and 3b. Details of the structural analyses show that five highly significant RNA stem-loops in the UFR can be modeled into a compact superstructure by the interaction of two predicted pseudoknot structures. The folded superstructure comprising nt 44 to 330, with additional 22 nt downstream from this UFR, is suggested to serve as a ribosome landing pad (or an internal ribosomal entry site) in the cap-independent translation of the 3c of IBV. Intriguingly, the proposed structural motif of this coronavirus shares structural features similar to those proposed in a number of picornavirus mRNAs. Based on the common structural features, a plausible base pairing model between mRNA3 and 18 S rRNA is suggested, which is consistent with a general mechanism for regulation of internal initiation described in many picornaviruses.

Base Sequence↗
PubMed1996

Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions.

Two atomic level knowledge-based mean force interaction potentials (KBPs), a centrosymmetric burial position term and a long-range pairwise term, were developed. These were tested by comparing multiple configurations of three structurally unrelated proteins and were found successfully to (i) discriminate native state proteins from grossly misfolded structures in inverse folding tests, (ii) rank identify, using the KBP energy/r.m.s.d. correlation, native from progressively less native-like (compact and dilated) structures generated via molecular dynamics sampling, providing an energy gradient sloping from partially unfolded structures towards near-native states in inverse refinement tests (iii) smooth the overall potential energy surface in the region of dilated non-native structures by countering local minima of the in vacuo molecular mechanical potential and (iv) serve as a local minimum detector during simulated temperature quenching studies. These atomic KBPs discriminated native from non-native structures with greater overall sensitivity than did either a residue-based pairwise interaction potential or an effective solvation potential based on atomic contact volume occupancy. The KBPs presented here are immediately useful as a tool for selecting "good refinement candidates' from an arbitrary collection of protein configurations and may play a role in dynamic computational protein refinement.

Flavodoxin↗
PubMedDate not supplied

In vitro evaluation of a compact metabolic measurement instrument.

The ability of the Datex Deltatrac (Sensor-Medics, Anaheim, CA) to accurately measure oxygen consumption (VO2v) and carbon dioxide production (VCO2) was examined in vitro using the carbon dioxide addition and nitrogen dilution methods. The accuracy of respiratory quotient (RQ = VCO2/VO2) measurements was assessed using methanol combustion (RQ = 0.67). Both in the canopy (blow-by) and respirator (FiO2: 0.21-0.6, PEEP: 0-12 cm H2O) modes the Deltatrac's measurements of VO2 and VCO2 were within +/- 7% of values predicted from CO2 and N2 simulations. Similar results were obtained with methanol combustion. In vitro testing revealed that the Deltatrac accurately measures VO2 and VCO2 under a variety of simulated clinical conditions.

Calorimetry↗
PubMed2002

Fiber-optic infrared radiometer for accurate temperature measurements.

A fiber-optic radiometer is developed for accurate noncontact temperature measurements. Of compact and novel design, it is based on replacing the usual chopper with a simple shutter. The radiometer operates in a spectral range of 5-20 microm and uses a silver-halide IR-transmitting optical fiber. The radiometer has a temperature resolution of 0.1 degrees C, a time response of 200 ms, and a spatial resolution of approximately 1 mm. Theory, simulation, radiometer design and construction, and examples of experimental measurements are shown. The novel radiometer can be used in diverse applications in science, medicine, and industry.

Journal Article↗
PubMed2005

Development of a Bacillus sphaericus tablet formulation and its evaluation as a larvicide in the biological control of Culex quinquefasciatus.

This study aimed to analyze the final fermentation culture of Bacillus sphaericus 2362, standardize it and develop an active tablet formulation for use in urban mosquito breeding sites. It was performed in three phases: analysis and standardization of a B. sphaericus fermented culture; physical, chemical, and biological analysis of the active powder (solubility, residual humidity, particle size, resting angle, flowing off time, compacted density, and biological activity against Culex quinquefasciatus larvae); and the development of fast-disintegrating tablets. Five formulations with differing compositions were developed and a UV protector was added to the selected formulation. The formulation products with or without UV protector, as well as the active powder caused 100% larval mortality from 1 day to 2 months after a single treatment under simulated field conditions. These results show that the UV protector does not affect the initial larvicide activity of B. sphaericus, nor its persistence over a period of two months.

Animals↗
PubMed1981

The electrogenic Na-Ca exchange and the cardiac electrical activity. I--Simulation on Purkinje fibre action potential.

1. The effects of the current (iex) generated by the Na-Ca exchange mechanism have been investigated on the electrical activity of a cardiac cell using the model of MC ALLISTER et al. (1975) for the Purkinje fibre action potential (AP). 2. The reversal potential and the steady-state value of iex were described by the same equations as for the squid axon (MULLINS, 1976). The maximal intensity and the time constant of iex were extrapolated from experiments using frog hearts. 3. A compact program written with the Adams method in Fortran IV (PLANT, 1979) allowed a minicomputer to be used. 4. The addition of iex to the previous model induced a prolongation of the AP and a reduction of the duration of the diastolic phase. 5. Increasing the maximal steady-state amplitude of iex may lead to early after depolarizations and oscillatory behaviour. These effects can be prevented by adequate changes in the amplitude of some potassium outward currents. 6. It is concluded that : (i) alterations of the Na-Ca exchange, e.g., by cellular Na loading, should induce variations of both AP repolarization and diastolic phase durations and, consequently, alter the beating rate ; (ii) iex could interfere with the outward currents whose characteristics should be reconsidered.

Action Potentials↗
PubMed1999

Folding pathway of FKBP12 and characterisation of the transition state.

The folding pathway of human FKBP12, a 12 kDa FK506-binding protein (immunophilin), has been characterised. Unfolding and refolding rate constants have been determined over a wide range of denaturant concentrations and data are shown to fit to a two-state model of folding in which only the denatured and native states are significantly populated, even in the absence of denaturant. This simple model for folding, in which no intermediate states are significantly populated, is further supported from stopped-flow circular dichroism experiments in which no fast "burst" phases are observed. FKBP12, with 107 residues, is the largest protein to date which folds with simple two-state kinetics in water (kF=4 s(-1)at 25 degrees C). The topological crossing of two loops in FKBP12, a structural element suggested to cause kinetic traps during folding, seems to have little effect on the folding pathway. The transition state for folding has been characterised by a series of experiments on wild-type FKBP12. Information on the thermodynamic nature of, the solvent accessibility of, and secondary structure in, the transition state was obtained from experiments measuring the unfolding and refolding rate constants as a function of temperature, denaturant concentration and trifluoroethanol concentration. In addition, unfolding and refolding studies in the presence of ligand provided information on the structure of the ligand-binding pocket in the transition state. The data suggest a compact transition state relative to the unfolded state with some 70 % of the surface area buried. The ligand-binding site, which is formed mainly by two loops, is largely unstructured in the transition state. The trifluoroethanol experiments suggest that the alpha-helix may be formed in the transition state. These results are compared with results from protein engineering studies and molecular dynamics simulations (see the accompanying paper).

Binding Sites↗
PubMed2004

NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist: structural implications for the MHC II (I-Au)-peptide complex from docking calculations.

Experimental autoimmune encephalomyelitis can be induced in susceptible animals by immunodominant determinants of myelin basic protein (MBP). To characterize the molecular features of antigenic sites important for designing experimental autoimmune encephalomyelitis suppressing molecules, we report structural studies, based on NMR experimental data in conjunction with molecular dynamic simulations, of the potent linear dodecapeptide epitope of guinea pig MBP, Gln74-Lys75-Ser76-Gln77-Arg78-Ser79-Gln80-Asp81-Glu82-Asn83-Pro84-Val85 [MBP(74-85)], and its antagonist analogue Ala81MBP(74-85). The two peptides were studied in both water and Me(2)SO in order to mimic solvent-dependent structural changes in MBP. The agonist MBP(74-85) adopts a compact conformation because of electrostatic interactions of Arg78 with the side chains of Asp81 and Glu82. Arg78 is 'locked' in a well-defined conformation, perpendicular to the peptide backbone which is practically solvent independent. These electrostatic interactions are, however, absent from the antagonist Ala81MBP(74-85), resulting in great flexibility of the side chain of Arg78. Sequence alignment of the two analogues with several species of MBP suggests a critical role for the positively charged residue Arg78, firstly, in the stabilization of the local microdomains (epitopes) of the integral protein, and secondly, in a number of post-translational modifications relevant to multiple sclerosis, such as the conversion of charged arginine residues to uncharged citrullines. Flexible docking calculations on the binding of the MBP(74-85) antigen to the MHC class II receptor site I-A(u) using haddock indicate that Gln74, Ser76 and Ser79 are MHC II anchor residues. Lys75, Arg78 and Asp81 are prominent, solvent-exposed residues and, thus, may be of importance in the formation of the trimolecular T-cell receptor-MBP(74-85)-MHC II complex.

Alanine↗