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PubMed2003

3D-Lattice Monte Carlo simulations of model proteins. Size effects on folding thermodynamics and kinetics.

Recently, we devised an energy scale to vary systematically amino-acid residue-solvent interactions for Monte Carlo simulations of lattice-model proteins in water. For 27-mer proteins, the folding behavior varies appreciably with the choice of interaction parameters. We now perform similar simulations with 64-mers to study the size dependence of the optimal energy parameter set for representing realistic behavior typical of many real proteins (i.e. fast folding and high cooperativity for single chains). We find that 64-mers are considerably more stable and more cooperative compared to 27-mers. The optimal interfacial-interaction-energy parameter set, however, is relatively size independent.

Amino Acid Sequence↗
PubMed2000

Simultaneous quantitative determination of electroporative molecular uptake and subsequent cell survival using gel microdrops and flow cytometry.

BACKGROUND: Electroporation is widely used to introduce molecules into cells, but conditions yielding maximal molecular uptake often result in low cell survival. We describe a high throughput method for analyzing populations of culturable cells simultaneously for molecular uptake and cell growth. METHODS: Cells are microencapsulated within agarose gel microdrops (GMDs), exposed to a polar tracer fluorescent molecule, electrically pulsed at various field strengths, and cultured. The GMDs are then analyzed at about 100,000 occupied GMDs per hour by flow cytometry for both uptake and microcolony formation. RESULTS: We demonstrate how the method can be used to optimize a parameter of interest (e.g., the applied field strength) with respect to both uptake and cell survival. Here, the optimal field strength is determined to be 1.7 kV/cm. Below this, there is lower molecular uptake. As the field strength is increased, the cell survival rate goes down. CONCLUSIONS: This method may be applicable to optimization of other electroporation parameters and alternative physical and chemical methods for cell loading.

Animals↗
PubMed1988

The biomechanics of javelin throwing: a review.

In this paper, the scientific literature and that on the sports sciences relevant to javelin throwing is critically reviewed. This is particularly timely because of the change in the specification of the javelin for the men's event, which was introduced by the IAAF in 1986. A full discussion of the aerodynamics of the javelin is presented with due consideration of the change in pitching moment characteristics that the rules change had brought about. The uses and limitations of current computer programs for simulating javelin flight, in order to estimate optimal release parameters, are profiled. Consideration is also given to the effects of wind velocity, air density, javelin weight and the flutter and spin of the javelin on its flight. The review further considers the optimization of release parameters, drawing upon computer simulations and field-based data. The effects of release speed, release height, release angle, release angle of attack and release pitch rate are assessed. The javelin throwing technique is discussed in relation to cinematographically derived data, including an evaluation of experimental procedures. The importance to successful performance of the grip, the run-up and transition phases, the cross over and delivery strides are each reviewed. Finally, some prognoses as to the direction of future research into this complex throwing skill are offered.

Air Movements↗
PubMed2006

Parameter estimation for stiff equations of biosystems using radial basis function networks.

BACKGROUND: The modeling of dynamic systems requires estimating kinetic parameters from experimentally measured time-courses. Conventional global optimization methods used for parameter estimation, e.g. genetic algorithms (GA), consume enormous computational time because they require iterative numerical integrations for differential equations. When the target model is stiff, the computational time for reaching a solution increases further. RESULTS: In an attempt to solve this problem, we explored a learning technique that uses radial basis function networks (RBFN) to achieve a parameter estimation for biochemical models. RBFN reduce the number of numerical integrations by replacing derivatives with slopes derived from the distribution of searching points. To introduce a slight search bias, we implemented additional data selection using a GA that searches data-sparse areas at low computational cost. In addition, we adopted logarithmic transformation that smoothes the fitness surface to obtain a solution simply. We conducted numerical experiments to validate our methods and compared the results with those obtained by GA. We found that the calculation time decreased by more than 50% and the convergence rate increased from 60% to 90%. CONCLUSION: In this work, our RBFN technique was effective for parameter optimization of stiff biochemical models.

Algorithms↗
PubMed2001

Short stature and truncal shortening in transfusion dependent thalassemia patients: results from a thalassemia center in Malaysia.

One of the major complications in patients with transfusion dependent thalassemia is growth impairment secondary to iron overload. We studied the growth status in 66 patients with beta-thalassemia major and HbE-beta thalassemia who were transfusion dependent, aged from 2 to 24 years, and 66 controls matched for sex and age. The prevalence of short stature in transfusion-dependent thalassemics was 54.5% compared to 4.5% in control group (p<0.001). Short stature was more prevalent in those above the age of 10 years in this study group (83.3% vs 16.7%). Transfusion dependent thalassemics with short stature were found to have significantly lower mean standing height standard deviation scores (SDS), sitting height SDS and subischial leg length SDS values (p<0.001). There was also a significant difference between the mean sitting height SDS and the mean subischial leg length SDS in our thalassemics with short stature, suggesting that the short stature was due to disproportionate truncal shortening. Serum ferritin levels were significantly higher in transfusion dependent thalassemics who were short compared to those who were of normal height (p = 0.002). However, the mean pre-transfusion hemoglobin levels did not differ significantly between patients with short stature and those with normal height (p = 0.216). The prevalence of short stature also did not differ significantly between those with beta-thalassemia major and those with HbE-beta thalassemia (p = 0.32). This study highlighted the importance of providing optimal treatment in these patients, including monitoring of growth parameters and optimizing iron chelation therapy.

Adolescent↗
PubMed1997

Transfer of macromolecules into living adult cardiomyocytes by microinjection.

Among techniques commonly used to deliver bioactive molecules into living cells, microinjection is a very efficient method. Microinjection has been used extensively for gene transfer into different cell types. We applied the microinjection technique to the adult rat ventricular cardiac muscle cells (AVC) in primary culture and optimized microinjection parameters and the appropriate cell culture conditions. We also optimized the use of particular agents (i.e. 2,3-butanedione monoxime, verapamil) for the prevention of the cell damage caused by the micropuncture. We obtained the expression of a CMV-beta-galactosidase reporter gene in up to 20% of the injected cells with efficient maintenance of long term cell viability. Under our experimental conditions direct microinjection is a very advantageous technique to transfer macromolecules into living adult cardiac muscle cells and a powerful system to study and manipulate the biochemistry and molecular biology of the cardiac myocyte.

Age Factors↗
PubMed1996

Modelling of force production in skeletal muscle undergoing stretch.

Many human movements involve eccentric contraction of muscles. Therefore, it is important that a theoretical model is able to represent the kinetic response of activated muscle during lengthening if it is to be applied to dynamic simulation of such movements. The so-called Hill and Distribution Moment models are two commonly used models of skeletal muscle. The Hill model is a phenomenological model based on experimental observations; the Distribution Moment model is based on the cross-bridge theory of muscle contraction. The ability of each of these models to predict the force-velocity relation has been considered previously; however, few attempts have been made to evaluate the force response of each model with respect to time during stretches at different velocities. The purpose of this study was to compare the predicted force-time responses of the Hill and Distribution Moment models to the actual force produced by the cat soleus during experimental iso-velocity stretches at maximal activation. Two stretch velocities were simulated: 7.2 and 400 mm s-1. Model parameters were derived from the literature where possible. In addition, model parameters were optimized to provide the best possible fit between model force predictions and experimental results at each velocity. The results of the study showed that using the Hill model, it was possible to describe qualitatively the force-time response of the muscle at both velocities of stretch using parameters derived from the literature. It was also possible to optimize a set of parameters for the Hill model to provide a quantitative description of the force-time response at each velocity. Using the Distribution Moment model, it was not possible to describe the force-time response of the muscle for both velocities using a single set of rate constants, suggesting that the cross-bridge theory, upon which the model is based, may have to be further evaluated for lengthening muscle. Further research is required to determine if the model results can be generalized to other muscles and other velocities of stretch.

Animals↗
PubMed2002

Optimization of multiple spin-echo sequences for 3D polymer gel dosimetry.

The overall performance of polymer gel dosimeters for three-dimensional radiation dosimetry is determined by the temporal and spatial stability of the gels, dose sensitivity and image quality with respect to both systematic and stochastic deviations. The dose resolution (D(p)delta) is determined by the dose sensitivity and the signal-to-noise ratio (SNR) in the dose images. The dose sensitivity can be altered by changing the chemical composition of the polymer gel. The SNR is determined by the scanner and the imaging sequence. In the dose verification of conformal radiotherapy treatments the chosen number of slices may reach a number of 10-20. For these experiments, to obtain a sufficient SNR within a reasonable measurement time using a certain MR scanner, the imaging sequence should be optimized. A few other studies have emphasized the importance of optimizing the imaging sequence with respect to dose resolution (D(p)delta) or SNR but do not give quantitative values for the optimal sequence parameters for scanning a polymer gel dosimeter in three dimensions. In this paper, it is proved that a multiple spin-echo sequence is preferable to a single spin-echo sequence. It is also shown that when using a multiple spin-echo sequence it is not the inter-echo time that should be optimized but the number of echoes. An algebraical expression is derived for the dose resolution in terms of sequence parameters. A mathematical formalism and look-up tables are provided that can be used to optimize both a single and a slice-selective multiple spin-echo sequence to acquire a set of dose images at various locations. The use of the optimization protocol is illustrated by some examples. The optimization protocol enables the user to derive the optimal sequence parameters to acquire a set of dose maps obtained by quantitative T2 imaging for each polymer gel dosimeter within the shortest time possible.

Acrylic Resins↗
PubMed1990

Increased light scattering resolution facilitates multidimensional flow cytometric analysis.

Multidimensional flow cytometry identifies cell populations as clusters in a space created by the analysis of multiple parameters simultaneously. Optimal use of this multidimensional space requires each of the individual parameters to provide additional information for cell population discrimination as well as maximum utilization of the dynamic range available for each parameter. In this study we improve the visualization of the information present in light scattering signals from leukocytes to facilitate multidimensional flow cytometric analysis. Optimization of cell preparation techniques are essential to obtain high resolution light scattering signals that give complete separation of the granulocytes, monocytes, and granular and nongranular lymphocytes. The angle at which the forward scattered light was collected was modified to enhance the separation between leukocyte populations. Although orthogonal light scattering signals separate granular and nongranular lymphocytes, the resolution and dynamic range could not be displayed using linear or logarithmic functions. By applying a polynomial function to the orthogonal light scattering signals, all leukocyte populations could be displayed while maintaining high resolution. The combination of high resolution light scattering with a nonlinear display resulted in an equally spaced distribution of the cell populations distinguished by correlating forward and orthogonal light scattering signals. Using this approach, peripheral blood neutrophils, eosinophils, basophils, monocytes, and granular and nongranular lymphocytes were shown to occupy distinct locations in the correlation of orthogonal and forward light scattering. Surprisingly, the basophilic granulocytes were located close to granular lymphocytes and monocytes rather than near neutrophils and eosinophils.

Antigens, CD↗
PubMed2006

Multithreaded cardiac CT.

Phase-correlated CT, as it is used for cardiac imaging, is the most popular and the most important but also the most demanding special CT application in the clinical routine, today. Basically, it fulfills the four-dimensional imaging task of depicting a quasiperiodically moving object at any desired motion phase with significantly reduced motion artifacts. Although image quality with phase-correlated reconstruction is far better than with standard reconstruction, there are motion artifacts remaining and improvements of temporal resolution are required. As a well-known alternative to simply decreasing rotation time, we consider a spiral cone-beam CT scanner that has G x-ray guns and detectors mounted. We call this a multisource or a multithreaded CT scanner. Aiming for improved temporal resolution the relative temporal resolution tau, which measures the fraction of a motion period that enters the image, is studied as a function of the motion rate (heart rate) and the degree of scan overlap (pitch value) for various configurations. The parameters to optimize are the number of threads G and the interthread parameters delta alpha and delta z, which are the angular and the longitudinal separation between adjacent threads, respectively. To demonstrate the improvements approximate image reconstruction of multithreaded raw data is performed by using a generalization of the extended parallel back projection cone-beam reconstruction algorithm [Med. Phys. 31(6), 1623-1641 (2004)] to the case of multithreaded CT. Reconstructions of a simulated cardiac motion phantom and of simulated semi-antropomorphic phantoms are presented for two and three threads and compared to the single-threaded case to demonstrate the potential of multithreaded cardiac CT. Patient data were acquired using a clinical double-threaded CT scanner to validate the theoretical results. The optimum angle delta alpha between the tubes is 90 degrees for a double-threaded system, and for triple-threaded scanners it is 60 degrees or 120 degrees. In all cases, delta z = 0 results as an optimum, which means that the threads should be mounted in the same transversal plane. However, the dependency of the temporal resolution on delta z is very weak and a longitudinal separation delta z not = 0 would not deteriorate image quality. The mean temporal resolution achievable with an optimized multithreaded CT scanner is a factor of G better than the mean temporal resolution obtained with a single-threaded scanner. The standard reconstructions showed decreased cone-beam artifacts with multithreaded CT compared to the single-threaded case. Our phase-correlated reconstructions demonstrate that temporal resolution is significantly improved with multithreaded CT. The clinical patient data confirm our results.

Algorithms↗
PubMed2006

Electron group functions for the analysis of the electronic structures of molecules.

The electronic structure of a vast majority of molecular systems can be understood in terms of electron groups and their wave functions. They serve as a natural basis for bringing intuitive chemical and physical concepts into quantum chemical calculations. This article considers the general electron group functions formalism as well as its simple geminal version. We try to characterize the wave function with the group structure and its capabilities in actual calculations. For this purpose we implement a variational method based on the wave function in the form of an antisymmetrized product of strongly orthogonal group functions and perform a series of electronic structure calculations for small molecules and model systems. The most important point studied is the relation between the choice of electron groups and the results obtained. We consider energetic characteristics as well as optimal geometry parameters. In view of practical importance, the structure of variationally optimized local one-electron states is considered in detail as well as intuitive characteristics of chemical bonds.

Journal Article↗
PubMed1998

Absolute metabolite quantification by in vivo NMR spectroscopy: V. Multicentre quantitative data analysis trial on the overlapping background problem.

The goal of this study was to establish the best approach for quantifying nuclear magnetic resonance (NMR) lines, that in the frequency domain are overlapping with broad, unwanted background features. To perform the quantitative data analysis in a controlled way, test signals were designed and utilised, derived from two different real-world in vivo nuclear magnetic resonance signals. One of the main conclusions of the study was that the quantification methods currently available to the biomedical research groups can deliver the correct values of the quantitative parameters, but that great care should be taken in using optimal input parameters for the computer programs concerned.

Bayes Theorem↗