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Results for “Compaction simulator”

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At least 667 records · Page 37Linked to original sources

PubMed2000

Dorsoventral compartmentalization of mesoderm in heart-forming area of chick embryo.

In early chick development (stages 5-8) the seemingly homogeneous mesoderm in the heart-forming area splits to somatic and splanchnic cardiogenic layers. Little is known about dorsoventral compartmentalization before splitting. Electron microscopic analysis shows the early dorsoventral polarization of precardiomyocytes. The dorsal compartment has epithelial and the ventral compartment mesenchymal features with numerous protrusions. At stage 5+-6 staining for wheat germ agglutinine (WGA) transiently demarcates the ventral part of mesoderm. The glycosomes (beta-glycogen) show a dorsoventral gradient in the mesoderm of the cardiogenic field during the initial step of the compaction. The differential expression of glycosomes depends on the activity of glycogen synthase kinase 3-beta, a component of the wnt-signaling pathway, and might in this spatiotemporal developmental window be involved in the commitment of presumptive cardiogenic and somatic cells. To verify this hypothesis simulation experiments with LiCl in vitro were carried out. The normal splitting of the mesoderm and the development of heart primordia were disturbed. Blocking the receptors of WGA by WGA in vitro at stage 5-5+ perturbs the migration of mesoderm to anterio-medial direction. It appears that early specification of dorsal and ventral compartments of the mesoderm in the heart-forming area correlates with the gradient of glycosomes. Our results suggest that the target of LiCl action (glycogen synthase kinase 3-beta) might be involved in the specification of heart primordia and that WGA receptors mediate the migration of mesoderm to the anteriomedial direction.

Animals↗

PubMed2006

An experimental methodology for monitoring contaminant transport through geotechnical centrifuge models.

In this paper, an attempt has been made to highlight an experimental methodology for monitoring contaminant transport through locally available silty soil and commercially available clay in geotechnical centrifuge models, for different compaction states. Use of multiple depth sensors to determine depth distribution of sodium chloride in the soil column has been detailed. The obtained results have been compared with argentometric method. To validate the centrifuge modelling, modelling of models has been used. The test setup developed can simulate contaminant transport mechanisms through the soil mass, which is approximately 10 m deep, over a period of 600 days. R (e) and P (e) are found to be N times higher in the centrifuge models. These numbers are found to be several orders less than unity. This indicates that laminar flow prevails and the dominating Cl(-) transport mechanism in centrifuge is diffusion. The study also highlights the fact that the geotechnical centrifuge modelling can be used as a viable alternative to field scale experimentation.

Centrifugation↗

PubMedDate not supplied

The centroid approximation for mixtures: calculating similarity and deriving structure--activity relationships.

Compounds are often synthesized and tested as mixtures. We propose the idea that the descriptor representation of a mixture may be approximated as the descriptor average of its individual component molecules. This centroid approximation has several potential advantages: the representation is very compact, calculating similarities and deriving structure-activity relationships (SARs) of mixtures involves very little computation, and existing software can be directly applied to mixtures as if they were single molecules. Here we use the atom pair and topological torsion descriptors. We run several types of simulations using mixtures composed of druglike molecules from the MDL Drug Data Report database. We show that similarity searches using mixtures as queries and/or database entries yield reasonable results, with the caveat that a correction is necessary for mixture-mixture comparisons where at least one of the mixtures contains very diverse molecules. We also show that predictive SARs in the form of trend vectors can be derived from mixtures.

Journal Article↗

PubMed2003

Development of modified release diltiazem HCl tablets using composite index to identify optimal formulation.

This article reports the preparation of tartaric acid treated ispaghula husk powder for the development of modified release tablets of diltiazem HCl by adopting direct compression technique and a 32 full factorial design. The modified ispaghula husk powder showed superior swelling and gelling as compared to untreated powder. Addition of compaction augmenting agent such as dicalcium phosphate was found to be essential for obtaining tablets with adequate crushing strength. In order to improve the crushing strength of diltiazem HCl tablets, to modulate drug release pattern, and to obtain similarity of dissolution profiles in distilled water and simulated gastric fluid (pH 1.2), modified guar gum was used along with modified ispaghula husk powder and tartaric acid. A novel composite index, which considers a positive or a negative deviation from an ideal value, was calculated considering percentage drug release in 60, 300, and 540 min as dependent variables for the selection of a most appropriate batch. Polynomial equation and contour plots are presented. The concept of similarity factor (f2) was used to prove similarity of dissolution in water and simulated gastric fluid (pH 1.2).

Compressive Strength↗

PubMed2006

A detector head design for small-animal PET with silicon photomultipliers (SiPM).

Small-animal PET systems are now striving for sub-millimetre resolution. Current systems based upon PSPMTs and finely pixellated scintillators can be pushed to higher resolution, but at the expense of other performance parameters and a rapidly escalating cost. Moreover, depth of interaction (DOI) information is usually difficult to assess in such systems, even though this information is highly desirable to reduce the parallax error, which is often the dominant error for such high-resolution systems. In this study we propose a high-resolution detector head for a small-animal PET imaging system with intrinsic DOI information. Instead of a pixellated scintillator, our design is based upon the classic Anger camera principle, i.e. the head is constructed of modular layers each consisting of a continuous slab of scintillator, viewed by a new type of compact silicon photodetector. The photodetector is the recently developed silicon photomultiplier (SiPM) that as well as being very compact has many other attractive properties: high gain at low bias voltage, excellent single-photoelectron resolution and fast timing. A detector head of about 4 x 4 cm2 in area is proposed, constructed from three modular layers of the type described above. We perform a simulation study, using the Monte Carlo simulation package Geant4. The simulation results are used to optimize the geometry of the detector head and characterize its performance. Additionally, hit estimation algorithms are studied to determine the interaction position of annihilation photons correctly over the whole detector surface. The resulting detector has a nearly uniform efficiency for 511 keV photons of approximately 70% and an intrinsic spatial resolution of less than approximately 0.4 mm full width at half maximum (fwhm).

Animals↗

PubMed2025

Phylogenetic Methods Meet Deep Learning.

Deep learning (DL) has been widely used in various scientific fields, but its integration into phylogenetics has been slower, primarily due to the complex nature of phylogenetic data. The studies that apply DL to sequencing data often limit analyses to four-taxon trees. Many of these studies serve as "proof of principle" and perform similarly to traditional phylogeny reconstruction methods. New ways of using training data, such as encoding with compact bijective ladderized vectors or transformers, enable the handling of much larger trees and genomic data sets. This short perspective focuses on the application of DL in phylogenetics, introducing prevalent DL architectures. We highlight potential problems in the field by discussing the risks of using simulation-based training data and emphasize the importance of reproducibility and robustness in computational estimates. Finally, we explore promising research areas, including the combination of phylogenetics and population genetics in DL, the analysis of neighbor dependencies, and the potential to significantly reduce computational cost compared to traditional methods. This perspective illustrates the potential of DL in complementing traditional phylogeny reconstruction methods and aiding the advancement of phylogenetic analysis, especially in performing computationally demanding tasks such as model selection or estimating branch support values.

Humans↗

PubMed2006

Endogenous driving and synchronization in cardiac and uterine virtual tissues: bifurcations and local coupling.

Cardiac and uterine muscle cells and tissue can be either autorhythmic or excitable. These behaviours exchange stability at bifurcations produced by changes in parameters, which if spatially localized can produce an ectopic pacemaking focus. The effects of these parameters on cell dynamics have been identified and quantified using continuation algorithms and by numerical solutions of virtual cells. The ability of a compact pacemaker to drive the surrounding excitable tissues depends on both the size of the pacemaker and the strength of electrotonic coupling between cells within, between, and outside the pacemaking region. We investigate an ectopic pacemaker surrounded by normal excitable tissue. Cell-cell coupling is simulated by the diffusion coefficient for voltage. For uniformly coupled tissues, the behaviour of the hybrid tissue can take one of the three forms: (i) the surrounding tissue electrotonically suppresses the pacemaker; (ii) depressed rate oscillatory activity in the pacemaker but no propagation; and (iii) pacemaker driving propagations into the excitable region. However, real tissues are heterogeneous with spatial changes in cell-cell coupling. In the gravid uterus during early pregnancy, cells are weakly coupled, with the cell-cell coupling increasing during late pregnancy, allowing synchronous contractions during labour. These effects are investigated for a caricature uterine tissue by allowing both excitability and diffusion coefficient to vary stochastically with space, and for cardiac tissues by spatial gradients in the diffusion coefficient.

Action Potentials↗

PubMed2005

Patient self-attenuation and technologist dose in positron emission tomography.

Positron emission tomography (PET), with 511-keV radiation and long patient-uptake times, presents unique radiation safety concerns. This two-part study considers aspects of PET radiation safety as they relate to PET suite design, dose to the public, and technologist occupational dose. In the first part of the study, the self-attenuation of radiation by patients' bodies was quantified. The radiation exposure was measured at three positions from 64 patients injected with fluorine-18 fluorodeoxyglucose (FDG) during the uptake period. Compared with an in vitro control used as a point source, a significant decrease in exposure (>40% at 1 m) was observed due to nonuniform distribution of FDG and attenuation within the patients. The attenuation data are consistent with results from simulations [M. E. Phelps, "Comments and Perspectives," J. Nucl. Med. 45, 1601 (2004)] that treat the body as a uniform, water-filled cylinder. As distance is often the principal source of protection for 511-keV radiation, the considerable self-attenuation may allow for more compact PET suites. However, despite high patient self-attenuation, shielding, and standard precautionary measures, PET technologist occupational doses can remain quite high (approximately 12 mSv/year). The second part of this study tracked the daily dose received by PET technologists. Close technologist-patient interaction both during and following FDG administration, as much as 20 min/study, contribute to the high doses and point to the need for a more innovative approach to radiation protection for PET technologists.

Allied Health Personnel↗

PubMed1995

First-principles calculation of the folding free energy of a three-helix bundle protein.

The folding and unfolding of a three-helix bundle protein were explored with molecular-dynamics simulations, cluster analysis, and weighted-histogram techniques. The folding-unfolding process occurs by means of a "folding funnel," in which a uniform and broad distribution of conformational states is accessible outside of the native manifold. This distribution narrows near a transition region and becomes compact within the native manifold. Key thermodynamic steps in folding include initial interactions around the amino-terminal helix-turn-helix motif, interactions between helices I and II, and, finally, the docking of helix III onto the helix I-II subdomain. A metastable minimum in the calculated free-energy surface is observed at approximately 1.5 times the native volume. Folding-unfolding thermodynamics are dominated by the opposing influences of protein-solvent energy, which favors unfolding, and the overall entropy, which favors folding by means of the hydrophobic effect.

Amino Acid Sequence↗

PubMed1994

Map formation in proprioceptive cortex.

Current understanding of feature maps in proprioceptive cortex is quite limited. To complement experimental studies, we developed a computational model of map formation in proprioceptive cortex. Muscle length and tension from six muscle groups controlling the position of a model arm in three-dimensional space served as input to the simulated cortex. The resultant feature map consisted of regularly spaced clusters of cortical columns representing individual muscle lengths and tensions. Cortical units became tuned to plausible combinations of tension and length, and multiple representations of each muscle group were present. The map was organized such that compact regions within which all muscle group lengths and tensions are represented could be identified. Most striking was the observation that, although not explicitly present in the input, the cortical map developed a representation of the three-dimensional space in which the arm moved. These findings represent testable predictions about proprioceptive cortex, and may also help clarify some organizational issues concerning primary motor cortex.

Arm↗

PubMed2003

Development of a fluorescence detection system using optical parametric oscillator (OPO) laser excitation for in vivo diagnosis.

In this work, the development and applications of a fluorescence detection system using optical parametric oscillator (OPO) laser excitation for in vivo disease diagnosis including oral carcinoma are described. The optical diagnosis system was based on an OPO laser for multi-wavelength excitation and time-resolved detection. The pulsed Nd-YAG-pumped OPO laser system (6 ns, 20 Hz) is compact and has a rapid, broad, and uniform tuning range. Time-gated detection of intensified charge-coupled device (ICCD) making use of external triggering was used to effectively eliminate the laser scattering and contribute to the highly sensitive in vivo measurements. Artificial tissue-simulating phantoms consisting of polystyrene microspheres and tissue fluorophores were tested to optimize the gating parameters. 51-ns gate width and 39-ns gate delays were determined to be the optimal parameters for sensitive detection. In vivo measurements with the optical diagnosis system were applied to esophagus, stomach, and small intestine using an endoscope in canine animal studies. The rapid tuning capability of the optical diagnosis system contributed greatly to the optimization of wavelength for the observation of porphyrin in the small intestine. When the small intestine was thoroughly washed with water, the emission band which corresponds to porphyrin disappeared. Based on this observation, it was concluded that the detected signal was yielded by porphyrin-containing bile secretion. Also, multispectral analyses using multiple excitations from 415 to 480 nm at 5 nm intervals confirmed the porphyrin detection in the small intestine. The optical diagnosis system was also applied to the detection of human xenograft of oral carcinoma in mice using 5-aminolevulinic acid (5-ALA) which is a photodynamic therapy (PDT) drug. Significant differences in protoporphyrin IX fluorescence intensity between normal and tumor tissue could be obtained 2 hours after the injection of 5-ALA into mice due to the preferential accumulation of 5-ALA in tumors. Results reported herein demonstrate potential capabilities of the LIF-OPO system for in vivo disease diagnosis.

Animals↗

PubMed2001

Objective laparoscopic skills assessments of surgical residents using Hidden Markov Models based on haptic information and tool/tissue interactions.

UNLABELLED: Laparoscopic surgical skills evaluation of surgery residents is usually a subjective process, carried out in the operating room by senior surgeons. By its nature, this process is performed using fuzzy criteria. The objective of the current study was to develop and assess an objective laparoscopic surgical skill scale using Hidden Markov Models (HMM) based on haptic information, tool/tissue interactions and visual task decomposition. METHODS: Eight subjects (six surgical trainees: first year surgical residents 2 x R1, third year surgical residents 2 x R3 fifth year surgical residents 2 x R5; and two expert laparoscopic surgeons: 2 x ES) performed laparoscopic cholecystectomy following a specific 7 steps protocol on a pig. An instrumented laparoscopic grasper equipped with a three-axis force/torque sensor located at the proximal end with an additional force sensor located on the handle, was used to measure the forces and torques. The hand/tool interface force/torque data was synchronized with a video of the tool operative maneuvers. A synthesis of frame-by-frame video analysis was used to define 14 different types of tool/tissue interactions, each one associated with unique force/torque (F/T) signatures. HMMs were developed for each subject representing the surgical skills by defining the various tool/tissue interactions as states and the associated F/T signatures as observations. The statistical distance between the HMMs representing residents at different levels of their training and the HMMs of expert surgeons were calculated in order to generate a learning curve of selected steps during laparoscopic cholecystectomy. RESULTS: Comparison of HMM's between groups showed significant differences between all skill levels, supporting the objective definition of a learning curve. The major differences between skill levels were: (i) magnitudes of F/T applied (ii) types of tool/tissue interactions used and the transition between them and (iii) time intervals spent in each tool/tissue interaction and the overall completion time. The objective HMM analysis showed that the greatest difference in performance was between R1 and R3 groups and then decreased as the level of expertise increased, suggesting that significant laparoscopic surgical capability develops between the first and the third years of their residency training. The power of the methodology using HMM for objective surgical skill assessment arises from the fact that it compiles enormous amount of data regarding different aspects of surgical skill into a very compact model that can be translated into a single number representing the distance from expert performance. Moreover, the methodology is not limited to in-vivo condition as demonstrated in the current study. It can be extended to other modalities such as measuring performance in surgical simulators and robotic systems.

Animals↗

PubMed1997

Computer simulations of prebiotic evolution.

This paper is a review of our previous work on the field of possible ways of prebiotic evolution. We propose an algorithm providing sequences of model proteins with rapid folding into a given native conformation. Thermodynamical analysis shows that the increase in speed is matched by an increase in stability: the evolved sequences are much more stable in their native conformation than the initial random sequence. We discuss a possible origin of the first biopolymers, having stable unique structure. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact in order to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences of model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structure of first biopolymers could have evolved as a side effect of a nonspecific physico-chemical factors acting at the prebiotic stage of evolution.

Algorithms↗

PubMed2005

Precise fabrication of nanomaterials: a nonlinear dynamics approach.

Modeling of the precise fabrication in the self-assembling of particles is studied using the nonlinear Langevin equation system. The numerical simulation showed a marked ordering of the particles as a function of time after some induction period. The abnormally enlarged fluctuation was found around the start of the evident ordering. After the fluctuation, a sudden increase of the cluster size was observed. The results corresponded well to the dynamics due to the formation of the critical cluster. The shape of the critical cluster around the enlarged fluctuation was not compact and showed fractal-like structures. The fluctuation of the cluster size around the formation of the critical cluster was explained by the anomalous fluctuation theorem for the generalized Langevin equation. The characterization of the stochastic dynamics of the critical clusters rationalized the concept of dynamic templating for the fabrication technique of the self-assembling of nanoparticles, that is, the structural constraint on the particle assembly by externally adding the resonance frequencies that match with the localized nonlinear vibrational modes of the target structures originating from thermal (Brownian) activation.

Computer Simulation↗

PubMed2004

Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited.

Statistical-thermodynamic models for the excluded volume interaction between an unfolded polypeptide chain and a hard sphere or hard rod cosolute are presented, permitting estimation of the free energy of transfer of a polypeptide chain with fixed radius of gyration from a dilute (ideal) solution to a solution containing volume fraction of either cosolute. Also presented is a general thermodynamic description of the equilibrium between a unique native state and a manifold of unfolded or partially unfolded states of a protein distinguished by their respective radii of gyration. Together with results of a Monte Carlo calculation of the distribution of radii of gyration of four different unfolded proteins published by Goldenberg in 2003, these models are used to estimate the effect of intermolecular excluded volume upon an experimentally measurable apparent two-state constant for equilibrium between native and nonnative conformations of each of the four proteins, and upon the experimentally measurable root mean-square radius of gyration of the unfolded protein. Model calculations predict that addition of inert cosolutes at volume fractions exceeding 0.1 stabilizes the native state relative to unfolded states by an amount that increases strongly with and with the size of the native protein relative to the size of inert cosolute, and results in significant compaction of the manifold of unfolded states. Predicted effects are in qualitative and/or semiquantitative accord with the results of several published experimental studies.

Binding Sites↗

PubMed1997

Protein folding simulations with genetic algorithms and a detailed molecular description.

We have explored the application of genetic algorithms (GA) to the determination of protein structure from sequence, using a full atom representation. A free energy function with point charge electrostatics and an area based solvation model is used. The method is found to be superior to previously investigated Monte Carlo algorithms. For selected fragments, up to 14 residues long, the lowest free energy structures produced by the GA are similar in conformation to the corresponding experimental structures in most cases. There are three main conclusions from these results. First, the genetic algorithm is an effective method for searching amongst the compact conformations of a polypeptide chain. Second, the free energy function is generally able to select native-like conformations. However, some deficiencies are identified, and further development is proposed. Third, the selection of native-like conformations for some protein fragments establishes that in these cases the conformation observed in the full protein structure is largely context independent. The implications for the nature of protein folding pathways are discussed.

Algorithms↗

PubMed1989

Solution structure of recombinant hirudin and the Lys-47----Glu mutant: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study.

The solution structure of recombinant wild-type hirudin and of the putative active site mutant Lys-47----Glu has been investigated by nuclear magnetic resonance (NMR) spectroscopy at 600 MHz. The 1H NMR spectra of the two hirudin variants are assigned in a sequential manner with a combination of two-dimensional NMR techniques. Some assignments made in our previous paper [Sukumaran, D. K., Clore, G. M., Preuss, A., Zarbock, J., & Gronenborn, A. M. (1987) Biochemistry 26, 333-338] were found to be incorrect and are now corrected. Analysis of the NOE data indicates that hirudin consists of an N-terminal compact domain (residues 1-49) held together by three disulfide linkages and a disordered C-terminal tail (residues 50-65) which does not fold back on the rest of the protein. This last observation corrects conclusions drawn by us previously on hirudin extracted from its natural source, the leech Hirudo medicinalis. The improved sensitivity of the 600-MHz spectrometer relative to that of our old 500-MHz spectrometer, the availability of two variants with slightly different chemical shifts, and the additional information arising from stereospecific assignments of methylene beta-protons and methyl protons of valine have permitted the determination of the solution structure of hirudin with much greater precision than before. Structure calculations on the N-terminal domain using the hybrid distance geometry-dynamical simulated annealing method were based on 685 and 661 approximate interproton distance restraints derived from nuclear Overhauser enhancement (NOE) data for the wild-type and mutant hirudin, respectively, together with 16 distance restraints for 8 backbone hydrogen bonds identified on the basis of NOE and amide NH exchange data and 26 phi backbone and 18 chi 1 side-chain torsion angle restraints derived from NOE and three-bond coupling constant data. A total of 32 structures were computed for both the wild-type and mutant hirudin. The structure of residues 2-30 and 37-48 which form the core of the N-terminal domain is well determined in both cases with an average atomic rms difference between the individual structures and the respective mean structures of approximately 0.7 A for the backbone atoms and approximately 1 A for all atoms. As found previously, the orientation of the exposed finger of antiparallel beta-sheet (residues 31-36) with respect to the core could not be determined on the basis of the present data due to the absence of any long-range NOEs between the exposed finger and the core.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed2005

Preparation and characteristics of a calcium magnesium silicate (bredigite) bioactive ceramic.

In this study, new bredigite (Ca7MgSi4O16) ceramics were prepared by sintering sol-gel-derived bredigite powder compacts at 1350 degrees C for 8 h. The bending strength, fracture toughness and Young's modulus were about 156 MPa, 1.57 MPa m(1/2) and 43 GPa, respectively. The in vitro bioactivity of the bredigite ceramics was evaluated by investigating the apatite-formation ability in simulated body fluid (SBF) and the effect of ionic products from bredigite dissolution on the mouse fibroblasts cell line L929. In addition, the in vitro biocompatibility of the bredigite ceramics was evaluated by osteoblasts adhesion and proliferation assay. The results showed that bredigite ceramics could induce HAp formation in SBF. The products from bredigite dissolution significantly promoted cell growth at a certain concentration range. Furthermore, osteoblasts adhered and spread well on bredigite ceramics, and osteoblasts proliferation on bredigite ceramics was obvious.

Animals↗