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 721 records · Page 40Linked to original sources

PubMed1983

A highly simplified horizontal electrophoretic apparatus including a handmade power supply and its application.

An extremely simplified electrophoretic apparatus and power supply have been introduced for horizontal (flat-bed) electrophoresis and isoelectrofocusing. The electrophoretic apparatus consisted of a buffer tray with a plastic food container in which a gel glass plate attached to two removable bar electrodes with rubber bands was submerged. The removable bar electrode consisted of an acrylic bar plate containing holes to which platinum wire was attached. The power supply simply contained a bridge diode, fuse, capacitor, and output terminals which were also assembled in a small plastic food container. Since the output electric potential of the power supply was constant pulse dc 90 V (in the absence of a capacitor) or 140 V (in the presence of a capacitor) at 100 V ac input, the following equation was experimentally derived to control the electrophoretic current: I (mA) = aD + b, I (mA) = kF. In these, I, a, D, k, and F were electrophoretic current, constant, distance between positive and negative electrodes, constant, and dilution factor of the electrophoretic buffer which was proportional to buffer concentration, respectively. These equations indicate that electrophoretic current can be controlled by the changes of electrode distance and buffer dilution. The latter equation was theoretically derived from the theory of electrolyte conductance and Ohm's law and was simulated with a microcomputer. With the apparatus and power supply, agarose gel electrophoresis of DNA and discontinuous polyacrylamide gel electrophoresis of protein samples were successfully carried out. The construction and assembly of the system can be easily carried out in a laboratory without any special tools and machines. The high cost performance, compactness, and simplicity were superior points of this system. The applicability of the equation I = kF to tube gel and vertical slab gel electrophoresis was tested. The rheostat usage made it easy for the power supply to change dc-output potential without spoiling its cost performance. A convenient sample slot-former and gel preparation with it are also described.

Computers↗

PubMed2003

Nonlinear simulation of tumor growth.

We study solid tumor ( carcinoma) growth in the nonlinear regime using boundary-integral simulations. The tumor core is nonnecrotic and no inhibitor chemical species are present. A new formulation of the classical models [18,24,8,3] is developed and it is demonstrated that tumor evolution is described by a reduced set of two dimensionless parameters and is qualitatively unaffected by the number of spatial dimensions. One parameter describes the relative rate of mitosis to the relaxation mechanisms (cell mobility and cell-to-cell adhesion). The other describes the balance between apoptosis (programmed cell-death) and mitosis. Both parameters also include the effect of vascularization. Our analysis and nonlinear simulations reveal that the two new dimensionless groups uniquely subdivide tumor growth into three regimes associated with increasing degrees of vascularization: low (diffusion dominated, e.g., in vitro), moderate and high vascularization, that correspond to the regimes observed in vivo. We demonstrate that critical conditions exist for which the tumor evolves to nontrivial dormant states or grows self-similarly (i.e., shape invariant) in the first two regimes. This leads to the possibility of shape control and of controlling the release of tumor angiogenic factors by restricting the tumor volume-to-surface-area ratio. Away from these critical conditions, evolution may be unstable leading to invasive fingering into the external tissues and to topological transitions such as tumor breakup and reconnection. Interestingly we find that for highly vascularized tumors, while they grow unbounded, their shape always stays compact and invasive fingering does not occur. This is in agreement with recent experimental observations [30] of in vivo tumor growth, and suggests that the invasive growth of highly-vascularized tumors is associated to vascular and elastic anisotropies, which are not included in the model studied here.

Animals↗

PubMed2004

Translocation of a beta-hairpin-forming peptide through a cylindrical tunnel.

We use Langevin dynamics simulations of a minimalist off-lattice model to study the translocation of a beta hairpin forming peptide through a tunnel that mimics the exit tunnel in a ribosome. We have computed the free energy of the peptide as a function of its position relative to the tunnel exit and also studied the properties of the conformational ensemble, when the peptide's position is restricted at different points along the tunnel. Confining the peptide within a sufficiently wide tunnel stabilizes the folded state. The protein then remains folded as it moves towards the tunnel exit. However, when the diameter D of the tunnel is below a certain critical value D(c), confinement destabilizes the folded state and forces the peptide to assume an extended configuration. In this case, as the peptide progresses towards the tunnel exit and eventually leaves the tunnel, it goes through a series of compact, misfolded conformations and eventually folds when it gets close to the exit. The critical tunnel diameter D(c) is comparable to the width of ribosomal tunnels. Our results suggest that co-translational folding is probably not universal, but rather a protein-specific phenomenon.

Computer Simulation↗

PubMed2006

A probabilistic approach to compact steady-state kinetic equations for enzymic reactions.

We describe a method for deriving kinetic equations based on the simplification of a complex graphical scheme of steady-state enzymic reactions to one that is comprised of an unbranched pathway. It entails compressing unbranched multi-step sequences into one step, and fusing some graph nodes into a single node. The final form of the equations is compact and well structured, and it simplifies the choice of independent kinetic parameters. The approach is illustrated by an analysis of representative two- and three-substrate reactions.

Animals↗

PubMed1996

Molten globule-like state of cytochrome c under conditions simulating those near the membrane surface.

Methanol-induced conformational transitions in cytochrome c have been studied by near- and far-UV circular dichroism, Trp fluorescence, microcalorimetry, and diffusion measurements. The existence of at least two cooperative stages of transition has been shown. At the first stage, the native protein is transformed into an intermediate which has only traces of tertiary structure, but has a native-like secondary structure content and is relatively compact; i.e., it has properties of the molten globule state. On the second stage, the alcohol-induced molten globule is transformed into a more helical state, typical of proteins at high alcohol concentrations. The conditions at which the alcohol-induced molten globule exists (moderately low pH and moderately low dielectric constant) could be similar to those existing near negatively charged membrane surfaces. Consequently, these results might explain how the molten globule state can be achieved under physiological conditions.

Animals↗

PubMed2006

Early inner solar system impactors: physical properties of comet nuclei and dust particles revisited.

During the epoch of early bombardment, terrestrial planets have been heavily impacted by cometary nuclei and cometary dust particles progressively injected in the interplanetary medium. Stardust and Deep Impact missions confirm that the nuclei are porous, loosely consolidated objects, with densities below 1,000 kg m(-3), and that they often release small fragments of ices and dust. Recent numerical simulations of the light scattering properties of cometary dust particles indicate that they are highly porous, most likely fractal, and rich in absorbing organics compounds (with a mixture ratio of e.g. 33 to 60% in mass for comet Hale-Bopp). Taking into account the fact that porous structures survive more easily than compact ones during atmospheric entry, such results reinforce the scenario of the early terrestrial planets enrichment--in organics needed for life to originate--by comets.

Cosmic Dust↗

PubMed1998

Effect of masticatory cycles on apical leakage of obturated teeth.

This study investigated the effect of apical leakage due to masticatory cycles on root canal treatment. Twenty upper maxillary molars were first obturated using the warm vertical compaction technique. Four maxillary casts were then built, with each holding four of the sample molars. The molars were embedded in resin with the roots separated from the resin by means of a light silicon. The four remaining teeth served as controls and were not submitted to occlusal forces. A mechanical device to simulate masticatory cycles subjected the teeth to 0.5 x 10(6) cycles (group A), 10(6) cycles (group B), 2 x 10(6) cycles (group C), and 3 x 10(6) cycles (group D); the control was group E. The roots were placed in 2% methylene blue dye solution for 72 h and then sectioned longitudinally so that dye penetration could be measured. The mean values of dye penetration were: 3.70 +/- 0.69 mm, group A; 5.00 +/- 1.14 mm, group B; 6.00 +/- 1.01 mm, group C; 7.23 +/- 0.66 mm, group D; and 2.74 +/- 0.75 mm, group E. The value of dye penetration increased in correlation with the number of masticatory cycles. This in vitro study suggests the significant effect of masticatory loads on apical leakage.

Bite Force↗

PubMed2003

Development of silicone rubber hollow fiber membrane oxygenator for ECMO.

Silicone rubber hollow fiber membrane produces an ideal gas exchange for long-term ECMO due to nonporous characteristics. The extracapillary type silicone rubber ECMO oxygenator having an ultrathin hollow fiber membrane was developed for pediatric application. The test modules were compared to conventional silicone coil-type ECMO modules. In vitro experiments demonstrated a higher O2 and CO2 transfer rate, lower blood flow resistance, and less hemolysis than the conventional silicone coil-type modules. This oxygenator was combined with the Gyro C1E3 centrifugal pump, and three ex vivo experiments were conducted to simulate pediatric V-A ECMO condition. Four day and 6 day experiments were conducted in cases 1 and 2, respectively. Case 3 was a long-term experiment up to 2 weeks. No plasma leakage and stable gas performances were achieved. The plasma free hemoglobin was maintained within a normal range. This compact pump-oxygenator system in conjunction with the Gyro C1E3 centrifugal pump has potential for a hybrid total ECMO system.

Animals↗

PubMed1986

[The level of the musical loud sound and noise induced hearing impairment].

Recently, there has been an increasing number of reports concerning hearing impairment which musical loud sound is thought to be one of the causes. We are getting more of this musical loud sound as cassette tape recorders with head phones such as Walkman and so forth get popular as well as occasions to attending rock concerts and going to discotheques increase. This hearing impairment is generally called discotheque deafness and the following three types are considered; 1) deafness which have fixed by accumulation of loud sound over a long period of time as seen in people involved in musical performance such as rock musicians and mixing engineers; 2) abrupt noise induced hearing impairment triggered by loud sound and 3) state of deafness which is a progressing stage towards recovery of noise induced temporary threshold shift (NITTS), which occurs temporarily by a loud sound stimulus, and hearing ability recovers afterward. However, it is considered that these musical loud sounds not only changes every moment according to method of performing or type of music, but the volume of the sound actually reaching the auditory sense differs largely by locations and direction of the ear and speakers. So it becomes necessary to measure the accumulation of the noise which each individual is exposed under over a long period of time and at the same time carry out the regular medical checkups including hearing test to check the initiation and advancement of the noise induced hearing impairment. Then we can examine the relationship between loudness of the environmental noise and initiation and advancement of the hearing impairment. However, there has not been a device which is compact and measures noise exposure individually over a long period of time. So we have experimentally produced ultra compact noise dosimeter which we named Noise Badge, and with it we actually measured individual noise exposure over a long time in rock music, noise in discotheque and noisy factory. Then we examined the relationship between these loud sound and noise induced temporary threshold shift (NITTS) in discotheques and noise proof room using simulation of loud sound exposure. Moreover, we measured the most comfortable loudness level of head phones in each examine and different types of music with environmental noise in consideration, thus examining the relationship between musical loud sound and the hearing impairment.

Adaptation, Physiological↗

PubMed1991

Molecular mechanics of the formation of cholic acid micelles.

The molecular mechanics of cholic acid micelle formation were simulated using the Sybyl energy minimization program (MAXIMIN2), developed by Tripos Associates, interfaced with micro-Vax. Before energy minimization, the molecular dimensions of the cholic acid dodecamer C24H40O6, in terms of the unit cell axes a, b, and c in the cubic crystal class, had values of 13, 18, and 6.7 A, respectively. After energy minimization, at 9370 kcals/dodecamer, these values had increased to 21.6, 42.8 and 20.9 A. At an energy minimization level of 21,626 kcals/dodecamer, the micelle structure is stabilized by hydrophobic interaction, forming distinct horizontal channels along the b-axis, directing the carboxyl and hydroxyl groups toward the surface. These structural changes remain relatively constant as the process of energy minimization continues, down to the lowest energy level we considered, 9370 kcals/dodecamer. The cholic acid layers are highly dissimilar, forming channels of irregular size and shape in a somewhat helical structure. The carboxyl groups and phenanthrene rings are in a puckered orientation, which permits compact packing of the sandwiched multilayers. From the dimension of the channels, it is apparent that guest molecules, such as phospholipid, cholesterol, or inorganic calcium, can be incorporated into the micelle through more than one channel, forming inclusion complexes, such as gallstones.

Cholic Acid↗

PubMed2006

Immunohistochemical analysis of mucinous tubular and spindle cell carcinoma and papillary renal cell carcinoma of the kidney: significant immunophenotypic overlap warrants diagnostic caution.

Mucinous tubular and spindle cell carcinoma, a rare, recently described distinctive subtype of renal cell carcinoma, may have some morphologic similarities to the more common papillary renal cell carcinoma, particularly the basophilic (type 1) tumors with prominent solid growth pattern. Tumor circumscription, compact tubular architecture, focal papillations, mucin production and foam cells (features seen in both papillary renal cell carcinoma and mucinous tubular and spindle cell carcinoma), as well as spindle cell morphology, have resulted in some cases sent to us in consultation with a question of possible sarcomatoid papillary renal cell carcinoma. In this study, tissue microarrays with triplicate samples each from 27 mucinous tubular and spindle cell carcinomas and 20 papillary renal cell carcinomas were created to simulate experience in renal biopsy specimens. From immunohistochemistry (IHC) data, published in the contemporary literature, a panel consisting of alpha-methylacyl-CoA racemase (AMACR), cytokeratin 7 (CK7), epithelial membrane antigen (EMA), renal cell carcinoma marker (RCC Ma), CD10, high molecular weight cytokeratin (HMWK), and c-kit was designed to test its utility in differential diagnosis. The immunoreactivity in mucinous tubular and spindle cell carcinoma was AMACR 93%, CK7 81%, EMA 95%, RCC Ma 7%, CD10 15%, HMWK 15%, and c-kit 5% and in papillary renal cell carcinoma was AMACR 95%, CK7 65%, EMA 88%, RCC Ma 25%, CD10 80%, HWMK 15%, and c-kit 18%. This largest study to date on IHC of mucinous tubular and spindle cell carcinoma dispels the specificity of AMACR for papillary renal cell carcinoma among the RCC subtypes. The histogenesis of mucinous tubular and spindle cell carcinoma from the distal nephron continues to be debatable, as our study showed the expression of the proximal convoluted tubule-related marker AMACR among these tumors. Thus, in tumors with predominant compact tubular growth and focal papillary architectures, careful attention to the presence of a low-grade spindle cell population may be helpful in the distinction of mucinous tubular and spindle cell carcinoma, as the key immunohistochemical stains for papillary renal cell carcinoma are also expressed in this subtype of renal cell carcinoma.

Adenocarcinoma, Mucinous↗

PubMed1995

The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus.

The structure of a 34-nucleotide RNA pseudoknot that causes efficient -1 frameshifting in the messenger RNA of mouse mammary tumor virus has been investigated by NMR. Spectral assignment of the pseudoknot was facilitated by comparative NMR studies on the pseudoknot and on two smaller hairpin RNAs, and by using selective 13C labeling and 13C-edited NMR techniques. The three-dimensional structure of the pseudoknot has been determined. The frameshifter pseudoknot possesses structural features not observed in previously reported model pseudoknots. It has a compact structure with a pronounced bend at the junction of its G.C-rich stems. A single adenylate residue is intercalated between the two stems so that direct coaxial staking of the stems is not possible. The lack of an opposing nucleotide for the stacked, intervening adenylate creates a hinge in the pseudoknot. Most of the loop nucleotides are restrained by base staking interactions which keep the loops from adopting extended conformations. The sterically constrained loops direct the bending of the pseudoknot at the stem-stem junction. The roles of the intercalated adenylate and loop lengths in causing bending can explain their requirement for efficient frameshifting. Our NMR data also indicate that there are internal dynamics associated with the pseudoknot. The unique, compact structure and conformational flexibility of the pseudoknot may be required for recognition and favourable interaction with the translating ribosome, or with translation factors associated with the ribosome.

Base Sequence↗

PubMed2001

Biomechanical comparison of two racing wheelchair propulsion techniques.

PURPOSE: The purpose was to compare the conventional (CVT) and para-backhand (PBT) techniques used for racing wheelchair propulsion. Selected 3-D kinematic characteristics of the upper body and the electromyographic (EMG) signals of selected muscles during racing wheelchair propulsion over a roller system were examined. METHODS: Eight CVT and seven PBT elite performers served as the subjects. Each subject performed maximum effort pushing for 30 s at a load that simulated overground pushing. Two S-VHS camcorders (60 Hz) were used to obtain 3-D kinematic parameters and muscle activity was monitored using surface electrodes. RESULTS: The CVT was found to have significant shorter push time, smaller relative push time, and greater relative recovery time than the PBT. The CVT is a more compact stroke (smaller joint range of motion) and the PBT has a faster overall movement speed. Significant differences in arm positions were found between the two techniques at the instants of hand contact and hand release, and the upper arm was more internally rotated at these two instants in the CVT when compared with the PBT. The EMG data showed that large variations in muscle activation patterns existed in each technique group. In general, the flexor carpi radialis and triceps brachii were most active in the push phase. The upper trapezius and postero-middle deltoids were most active in the ascending recovery phase, whereas the extensor carpi radialis, biceps brachii, antero-middle deltoids, and pectoralis major were most active during the descending recovery phase. CONCLUSIONS: The greater push time and push angle associated with the PBT suggest that the PBT may be more suitable for endurance athletes who are less explosive in their pushing strokes. The greater time and angle allow PBT users the opportunity to transmit more force to the wheel.

Adult↗

PubMed1999

Periodicity-dependent stiffness of periodic hydrophilic-hydrophobic heteropolymers.

From extensive Monte Carlo simulations of a Larson model of perfectly periodic heteropolymers (PHP) in water, a striking stiffening is observed as the period of the alternating hydrophobic and hydrophilic blocks is shortened. At short period and low temperature needlelike conformations are the stable conformations. As temperature is increased thermal fluctuations induce kinks and bends. At large periods compact oligomeric globules are observed. From the generalized Larson prescription, originally developed for modeling surfactant molecules in aqueous solutions, we find that the shorter the period is the more stretched the PHP is. This novel effect is expected to stimulate polymer synthesis and trigger research on the rheology of aqueous periodic heteropolymer solutions.

Journal Article↗

PubMed2006

Mass fractal dimension of the ribosome and implication of its dynamic characteristics.

Self-similar properties of the ribosome in terms of the mass fractal dimension are investigated. We find that both the 30S subunit and the 16S rRNA have fractal dimensions of 2.58 and 2.82, respectively; while the 50S subunit as well as the 23S rRNA has the mass fractal dimension close to 3, implying a compact three-dimensional macromolecule. This finding supports the dynamic and active role of the 30S subunit in the protein synthesis, in contrast to the pass role of the 50S subunit.

Computer Simulation↗

PubMed1983

Computer graphics with computerized tomography for functional neurosurgery.

A computer graphics technique for computer-assisted stereotactic surgery is presented. The program is designed to aid the surgeon by presenting an on-line graphics display of stereotactic probes and electrodes superimposed on cross sections of the human brain stem. This technique simulates an otherwise blind surgical procedure on a graphics screen for use during surgery. An earlier system based around the DEC MINC-11 BA computer system has been used by the authors for the performance of stereotactic surgery with conventional ventriculography. This system has been upgraded and is now configured about an even more compact microprocessor-based hardware system with expanded graphics capabilities, which also allows its use with computerized tomography.

Brain Diseases↗

PubMed2003

Diffractive axicons in oblique illumination: analysis and experiments and comparison with elliptical axicons.

Axicons in oblique illumination produce broadened focal lines, a problem, e.g., in scanning applications. A compact mathematical description of the focal segment is presented, for the first time, to our knowledge, and the results are compared with elliptical axicons in normal illumination. In both cases, analytical expressions in the form of asteroid curves are obtained from asymptotic wave theory and caustic surfaces. The results are confirmed by direct diffraction simulations and by experiments. In addition we show that at a fixed angle an elliptical axicon can be used to compensate for the adverse effects of oblique illumination.

Journal Article↗

PubMed1991

Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics.

A long-standing problem of molecular biology is the prediction of globular protein tertiary structure from the primary sequence. In the context of a new, 24-nearest-neighbor lattice model of proteins that includes both alpha and beta-carbon atoms, the requirements for folding to a unique four-member beta-barrel, four-helix bundles and a model alpha/beta-bundle have been explored. A number of distinct situations are examined, but the common requirements for the formation of a unique native conformation are tertiary interactions plus the presence of relatively small (but not irrelevant) intrinsic turn preferences that select out the native conformer from a manifold of compact states. When side-chains are explicitly included, there are many conformations having the same or a slightly greater number of side-chain contacts as in the native conformation, and it is the local intrinsic turn preferences that produce the conformational selectivity on collapse. The local preference for helix or beta-sheet secondary structure may be at odds with the secondary structure ultimately found in the native conformation. The requisite intrinsic turn populations are about 0.3% for beta-proteins, 2% for mixed alpha/beta-proteins and 6% for helix bundles. In addition, an idealized model of an allosteric conformational transition has been examined. Folding occurs predominantly by a sequential on-site assembly mechanism with folding initiating either at a turn or from an isolated helix or beta-strand (where appropriate). For helical and beta-protein models, similar folding pathways were obtained in diamond lattice simulations, using an entirely different set of local Monte Carlo moves. This argues strongly that the results are universal; that is, they are independent of lattice, protein model or the particular realization of Monte Carlo dynamics. Overall, these simulations demonstrate that the folding of all known protein motifs can be achieved in the context of a single class of lattice models that includes realistic backbone structures and idealized side-chains.

Algorithms↗