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PubMed1977

Electron density and atomic number determination by computed tomography. Part I: Methods and limitations. Part II: A study of colloid cysts.

The feasibility of extracting electron density and effective atomic number from measurements of tissue in vitro and in vivo has previously been reported. The method requires scans to be obtained at two different beam energies. Optimization of these energies at 40 keV and 80 keV could enable a variation of 1 part in 400 of effective atomic number to be detected. The method is subject to certain limitations related to accuracy and sensitivity. The effect of varying the concentrations of certain atoms has been modelled demonstrating the limits below which variation in effective atomic number is unlikely to be detectable at acceptable radiation doses. A series of 12 patients with colloid cysts has been considered. All were treated by bilateral ventriculo-cisternostomy from one to 23 years ago. Nine of these patients, and the colloid cyst of one patient who died before treatment could be instituted, have been subjected to double energy scanning. The results suggest that the high attenuation values observed in colloid cysts are due to increased electron density and not to any increase in high atomic number elements. The cysts do not appear to change in size or content over long periods.

Adult↗
PubMed1982

[Control of recruitment of muscle motor units by optimization of energy expenditure].

In order to vary the force it is exerting a muscle calls upon a variable number of motor elements (spatial mobilisation) and modulates the contraction frequency of each of the fibers (temporal mobilisation). We have studied the frequency distribution as a function of the strength developed and of the elongation of the muscle, as well as the number of fibers recruited. Based on a double approach, experimental and mathematical, we propose a function controlling this two-fold muscular mobilisation: the optimisation of the energy expenditure. In other words, to develop a particular force, the number of fibers called upon and the contraction frequencies of each of them are such that the quantity of energy required by the muscle is a minimum. The study is limited to voluntary isometric muscular contraction. Using optimization techniques, numerical results corresponding to the model's simulation has been obtained by using a digital computer.

Energy Metabolism↗
PubMed1999

3D modeling, ligand binding and activation studies of the cloned mouse delta, mu; and kappa opioid receptors.

Refined 3D models of the transmembrane domains of the cloned delta, mu and kappa opioid receptors belonging to the superfamily of G-protein coupled receptors (GPCRs) were constructed from a multiple sequence alignment using the alpha carbon template of rhodopsin recently reported. Other key steps in the procedure were relaxation of the 3D helix bundle by unconstrained energy optimization and assessment of the stability of the structure by performing unconstrained molecular dynamics simulations of the energy optimized structure. The results were stable ligand-free models of the TM domains of the three opioid receptors. The ligand-free delta receptor was then used to develop a systematic and reliable procedure to identify and assess putative binding sites that would be suitable for similar investigation of the other two receptors and GPCRs in general. To this end, a non-selective, 'universal' antagonist, naltrexone, and agonist, etorphine, were used as probes. These ligands were first docked in all sites of the model delta opioid receptor which were sterically accessible and to which the protonated amine of the ligands could be anchored to a complementary proton-accepting residue. Using these criteria, nine ligand-receptor complexes with different binding pockets were identified and refined by energy minimization. The properties of all these possible ligand-substrate complexes were then examined for consistency with known experimental results of mutations in both opioid and other GPCRs. Using this procedure, the lowest energy agonist-receptor and antagonist-receptor complexes consistent with these experimental results were identified. These complexes were then used to probe the mechanism of receptor activation by identifying differences in receptor conformation between the agonist and the antagonist complex during unconstrained dynamics simulation. The results lent support to a possible activation mechanism of the mouse delta opioid receptor similar to that recently proposed for several other GPCRs. They also allowed the selection of candidate sites for future mutagenesis experiments.

Amino Acid Sequence↗
PubMed1999

[Scatter correction in myocardial thallium SPECT: needs for optimization of energy window settings in the energy window-based scatter correction techniques].

Accuracy and limitation of energy-window based scatter correction techniques have been evaluated for myocardial 201Tl SPECT by means of Monte Carlo simulation. In particular, projection view-dependency of energy distribution of the scattered photons was evaluated. Two geometrical configurations were simulated: namely a homogeneous cylindrical radioactivity located asymmetrically in a homogeneous cylindrical phantom, and a homogeneous ring radioactivity positioned at the myocardial region of a human thorax phantom. Energy spectra were recorded for each projection, and accuracy of the triple-energy window (TEW) method was then evaluation for both phantoms. The energy distribution of the scattered photons was apparently dependent on the projection view. TEW also demonstrated systematic overcorrection for the scatter because of multiple photo peaks around 80 KeV, and more importantly, the error was highly dependent on the projection view. The error reached to 35-38% for the view that is the closest to the 201Tl radioactivity (anterior view in case of the myocardial ring phantom), and was approximately 20% in the opposite view. This view-dependency of the error remained for other energy window settings, and was found to cause significant artifact in the reconstructed myocardial images, typically causing a defect in the anterior myocardial wall. Thus, this study demonstrated the need for optimizing the window settings for each projection view in all energy window-based scatter correction methods.

Heart↗
PubMed1992

An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin.

Based on the heavy-atom coordinates determined by the electron microscopy for the seven main helical regions of bacteriorhodopsin with the all-trans retinal isomer, energy optimizations were carried out for helix bundles containing the all-trans retinal and 13-cis retinal chromophores, respectively. A combination of simulated annealing and energy minimization was utilized during the process of energy optimization. It was found that the 7-helix bundle containing the all-trans isomer is about 10 kcal/mol lower in conformational energy than that containing the 13-cis isomer. An energetic analysis indicates that such a difference in energy is consistent with the observation that absorption of a 570-nm proton is required for the conversion of a bacteriorhodopsin from its all-trans to 13-cis form. It was also found that the above conversion process is accompanied by a significant conformational perturbation around the chromophore, as reflected by the fact that the beta-ionone ring of retinal moves about 5.6 A along the direction perpendicular to the membrane plane. This is consistent with the observation by Fodor et al. (Fodor, S.P.A., Ames, J.B., Gebhard, R., van der Berg, E.M.M., Stoeckenius, W., Lugtenburg, J., & Mathies, R.A., 1988, Biochemistry 27, 7097-7101). Furthermore, it is interesting to observe that although the retinal chromophore undergoes a significant change in its spatial position, the orientation of its transition dipole changes only slightly, in accord with experimental observations. In other words, even though orientation of the retinal transition dipole is very restricted, there is sufficient room, and degrees of freedom, for the retinal chromophore to readjust its position considerably. This finding provides new insight into the subtle change of the retinal microenvironment, which may be important for revealing the proton-pumping mechanism of bacteriorhodopsin. The importance of electrostatic and nonbonded interactions in stabilizing the 7-helix bundle structure has also been analyzed. Electrostatic interactions favor an antiparallel arrangement among adjacent helices. Nonbonded interactions, however, drive most of the closely packed helices into an arrangement in which the packing angles lie around -160 degrees, a value very near the -154 degrees value computed earlier as the most favorable packing arrangement of two poly(Ala) alpha-helices (Chou, K.-C., Némethy, G., & Scheraga, H.A., 1983, J. Phys. Chem. 87, 2869-2881). The structural features of the 7-helix bundle and their relationship to those found in typical 4-helix bundle proteins are also discussed.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2001

Optimizing the energy status of skin cells during solar radiation.

Ionizing- and ultraviolet-radiation cause cell damage or death by directly altering DNA and protein structures and by production of reactive oxygen species (ROS) and reactive carbonyl species (RCS). These processes disrupt cellular energy metabolism at multiple levels. The formation of DNA strand breaks activates signaling pathways that consume NAD, which can lead to the depletion of cellular ATP. Poly(ADP)-ribose polymerase (PARP-1) is the enzyme responsible for much of the NAD degradation following DNA damage, although numerous other PARPs have been discovered recently that await functional characterization. Studies on mouse epidermis in vivo and on human cells in culture have shown that UV-B radiation provokes the transient degradation of NAD and the synthesis of ADP-ribose polymers by PARP-1. This enzyme functions as a component of a DNA damage surveillance network in eukaryotic cells to determine the fate of cells following genotoxic stress. Additionally, the activation of PARP-1 results in the activation of a nuclear proteasome that degrades damaged nuclear proteins including histones. Identifying approaches to optimize these responses while maintaining the energy status of cells is likely to be very important in minimizing the deleterious effects of solar radiation on skin.

Animals↗
PubMed2004

Ab initio study of (13)C(alpha) chemical shift anisotropy tensors in peptides.

This study reports magnitudes and the orientation of the (13)C(alpha) chemical shift anisotropy (CSA) tensors of peptides obtained using quantum chemical calculations. The dependency of the CSA tensor parameters on the energy optimization of hydrogen atom positions and hydrogen bonding effects and the use of zwitterionic peptides in the calculations are examined. Our results indicate that the energy optimization of the hydrogen atom positions in crystal structures is necessary to obtain accurate CSA tensors. The inclusion of intermolecular effects such as hydrogen bonding in the calculations provided better agreement between the calculated and experimental values; however, the use of zwitterionic peptides in calculations, with or without the inclusion of hydrogen bonding, did not improve the results. In addition, our calculated values are in good agreement with tensor values obtained from solid-state NMR experiments on glycine-containing tripeptides. In the case of peptides containing an aromatic residue, calculations on an isolated peptide yielded more accurate isotropic shift values than the calculations on extended structures of the peptide. The calculations also suggested that the presence of an aromatic ring in the extended crystal peptide structure influences the magnitude of the delta(22) which the present level of ab initio calculations are unable to reproduce.

Anisotropy↗
PubMed1999

How much physical activity is needed for good health?

The Harvard Alumni study is reviewed critically with a view to resolving the apparent conflict between the conclusions drawn from this research and the current consensus on optimal patterns of physical activity for health. The optimal energy expenditure reported for the Harvard data set is less than at first appears, since the estimated expenditures are gross rather than net values. Further, the optimal energy expenditure has been over-estimated, because too high a cost was assumed for stair climbing, and sport involvement may also have been over-reported. The data do not as yet allow the assertion that benefit is obtained only from vigorous physical activity, and there seems little conflict with the current consensus on the benefits of moderate physical activity.

Energy Metabolism↗
PubMed1985

Radiotherapy of malignant melanoma.

The role of radiotherapy in the treatment of malignant melanoma is limited, and surgery generally forms the mainstay of medical practice. However, there are some circumstances in which radiotherapy should be considered the treatment of choice. Symptomatic metastatic lesions in bone or brain can effectively be palliated in a substantial proportion of instances. At the current stage of our knowledge, conventionally fractionated treatment of such lesions forms the standard against which other treatments should be measured. In contrast, metastatic lesions to skin or lymph nodes that do not overlie critical normal structures probably are better treated by high-dose-per-fraction techniques. Radiotherapy may play a definitive role in the treatment of lentigo maligna. The precise optimal energy of the beam to be used remains to be defined. Slightly more penetrating radiation appears to be required for lentigo maligna melanomas. Here, too, the optimal energy remains to be defined. The treatment of nonlentigenous melanomas primarily by radiotherapy is unproved in my opinion. Certainly, the data from the Princess Margaret Hospital is exciting, but I believe it must be corroborated by a well-designed trial before it can be accepted without question. Future directions in treatment of malignant melanoma are likely to include further trials of unconventional fractionation and the use of radiosensitizing agents in conjunction with radiotherapy. The time for dermatologists and radiation therapists to cooperate in such studies is at hand.

Aged↗
PubMed1995

Methodologic aspects of computed microtomography to monitor the development of osteoporosis in gastrectomized rats.

RATIONALE AND OBJECTIVES: We investigated the methodologic development of computed microtomography (CMT) for monitoring the development of osteoporosis in male Sprague-Dawley rats. METHODS: Eight rats were gastrectomized and eight rats were sham operated. Femurs, tibias, and tails were prepared, and CMT scans with spatial resolutions of 5-500 microns were made. Bone diameters, bone areas, and moments of inertia were determined from the CMT scans. Optimal slice position and the need for spatial resolution and energy optimization for future in vivo applications were investigated. RESULTS: Gastrectomy caused dramatic changes in the bone architecture of the tibia and the femur. The main features were vacuolization of the bone and reduced amounts of compact bone. Although the outer diameters of tubular bones (femur and tibia) were largely unaffected, their inner diameters were greatly increased following gastrectomy. Relative bone area and moment of inertia were greatly reduced. The optimal photon energy was 12 keV. CONCLUSION: It is possible to monitor gastrectomy-evoked changes in bone morphology at various sites in rats using CMT scanning. The changes are suggestive of osteoporosis. By optimizing the energy spectrum and spatial resolution, as well as choosing the proper slice position, it should be possible to keep absorbed doses low enough to avoid acute radiation injury in repeated in vivo measurements.

Animals↗
PubMed2006

Toward efficient photomodulation of conjugated polymer emission: optimizing differential energy transfer in azobenzene-substituted PPV derivatives.

We present fluorescence studies of quenching behavior in photoaddressable azobenzene-substituted derivatives of the fluorescent conjugated polymer poly(p-phenylenevinylene) (PPV). The azobenzene side chains partially quench the PPV fluorescence, and we have shown previously that the quenching efficiency is greater when the azobenzene side chains are cis than when they are trans. This effect provides a photoaddressable means of modulating the fluorescence intensity of PPV derivatives. To optimize the efficiency of photoinduced intensity modulation, it is important to understand the molecular nature of quenching by both trans- and cis-azobenzene side chains. Here we investigate the photophysical origins of quenching by the two isomers using steady-state and time-resolved fluorescence spectroscopy. We present results from the azobenzene-modified PPV derivative poly(2-methoxy-5-((10-(4-(phenylazo)phenoxy)decyl)oxy)-1,4-phenylenevinylene) (MPA-10-PPV) and two new related polymers, a copolymer lacking half of the azobenzene side chains and an analogue of MPA-10-PPV with a tert-butyl-substituted azobenzene. These studies reveal that steric interactions influence the extent of PPV emission quenching by trans-azobenzene but do not affect the efficient quenching by cis-azobenzene. The difference in dynamic quenching efficiencies between trans- and cis-azobenzene isomers is consistent with fluorescence resonance energy transfer. These results show that it is possible to control the efficiency of photoswitchable fluorescence modulation through specific structural variations designed to encourage or block quenching by trans-azobenzene. This is a promising approach to providing useful general guidelines for designing photomodulated PPV derivatives.

Journal Article↗
PubMed2004

The stabilometric evaluation of the erect stance. Energy-based optimal control in a numerical model.

AIM: This paper proposes an anthropomorphic model developed in a virtual context, useful to simulate the maintenance of the erect stance. Such a model can be built through a suitable software which can identify the geometry of the articular parts and place mechanical constraints (e.g. joints, spherical links, etc.) between the single elements. METHODS: Our approach can be described as the assembly of rigid parts linked at the joints. The control is given by internal torques at the joints and driven by strategy for the balance aimed to the least amount of total muscular energy spent. The anthropomorphic model proposed underlines and solves the typical problems of a system characterized by a multiple number of degree of freedom placed in erect stance and perturbed by phenomena of endogenous and exogenous nature. This model is developed via the coupling of 2 separate bi-dimensional models, one representing the sagittal plane and the other the frontal plane. The numerical tests were validated through experimental tests in a group of healthy volunteers. For this purpose we employed a stabilometric platform (force-plate) to record the statokinesigram (SKG) on the rest surface. RESULTS: The shapes of the stabilometric plots show a good spatial similarity between the experimental and simulated SKG. Both SKGs present a good range in the frontal plane with concentration of points in some areas (or attractors) in the experimental SKG, but not in the simulated one. The tests also showed a postural oscillation at low frequency (= 0.02Hz), probably due to the differential tiredness of groups of muscles or because of a delayed action of the neurological control. CONCLUSIONS: On the numerical simulations, we claim the suitability of the antropomorphic model for a general description of the maintenance of the erect stance. Despite the simplification, with our approach it is possible to simulate some of the main characteristics of the postural act. In particular, the length and the areas of the simulated SKG's are comparable with those of the experimental tests.

Journal Article↗
PubMed1996

Could oral erythromycin optimize high energy continuous enteral nutrition?

BACKGROUND: Intravenous erythromycin has previously been reported to stimulate gastric emptying, to inhibit gastric acid secretion and to stimulate pancreatic secretion during continuous gastric infusion of a liquid diet in healthy volunteers. AIM: The aim of this study was to evaluate the effects of oral erythromycin (160 mg/h) on gastrointestinal function under these conditions in seven healthy subjects. METHOD: This randomized double-blind cross-over study measured the gastric emptying rate of nutrients, gastric acid secretion, gastric pH, jejunal flow rate as well as biliopancreatic secretion and duodeno-caecal transit time during a 19.9 kJ/min continuous infusion of a nutrient solution (4.18 kJ/mL) in the antrum over a 6-h period by a perfusion method. RESULTS: The nutrition was well tolerated except by one subject with placebo perfusion. During the 6-period, total gastric volume and gastric volume of nutrient decreased during erythromycin administration by 22 +/- 8 and 22 +/- 6%, respectively. Gastric acid secretion was not modified by erythromycin. Lipase and bile salt outputs were significantly higher with erythromycin. The duodeno-caecal transit time was not statistically different with drug and placebo (169 +/- 15 and 146 +/- 19 min, respectively). CONCLUSION: During continuous gastric infusion of a liquid diet, the effect of oral erythromycin on gastric emptying could be useful to optimize cyclic enteral nutrition or to enhance the tolerance of enteral nutrition.

Administration, Oral↗
PubMed1997

Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search.

Five models by homology containing insertions and deletions and ranging from 33% to 48% sequence identity to the known homologue, and one high sequence identity (85%) model were built for the CASP2 meeting. For all five low identity targets: (i) our starting models were improved by the Internal Coordinate Mechanics (ICM) energy optimization, (ii) the refined models were consistently better than those built with the automatic SWISS-MODEL program, and (iii) the refined models differed by less than 2% from the best model submitted, as judged by the residue contact area difference (CAD) measure [Abagyan, R.A., Totrov, M.J. Mol. Biol. 268:678-685, 1997]. The CAD measure is proposed for ranking models built by homology instead of global root-mean-square deviation, which is frequently dominated by insignificant yet large contributions from incorrectly predicted fragments or side chains. We demonstrate that the precise identification of regions of local backbone deviation is an independent and crucial step in the homology modeling procedure after alignment, since aligned fragments can strongly deviate from the template at various distances from the alignment gap or even in the ungapped parts of the alignment. We show that a local alignment score can be used as an indicator of such local deviation. While four short loops of the meeting targets were predicted by database search, the best loop 1 target T0028, for which the correct database fragment was not found, was predicted by Internal Coordinate Mechanics global energy optimization at 1.2 A accuracy. A classification scheme for errors in homology modeling is proposed.

Models, Molecular↗
PubMed2003

Metabolic modulation and optimization of energy consumption in heart failure.

Chronic heart failure (CHF) is a common and disabling syndrome with a poor prognosis. It is a major and increasing public health problem. Angiotensin-converting enzyme inhibitors, diuretics, and digitalis are the standards treatments for CHF. Other drugs, such as beta-blockers, spironolactone, calcium antagonists, vasodilators, and antiarrhythmic agents are used to counteract the progression of the syndrome or to improve the hemodynamic profile. Despite optimum treatment with neurohumoral antagonists, prognosis of CHF remains poor; the patients complain of persistent reductions in their exercise capacity and quality of life. Fatigue and shortness of breath, two common and disabling symptoms in patient with CHF, are relatively independent from hemodynamic and neuroendocrine changes, although they seem to be related to the impairment of peripheral muscle metabolism and energetic phosphate production. Therefore, CHF is a complex metabolic syndrome in which the metabolism of cardiac and peripheral muscles is impaired and novel therapeutic strategies have been aimed at positive modulation with compounds such as carnitine, trimetazidine, and ranolazine.

Acetanilides↗
PubMed2003

Using optimized collision energies and high resolution, high accuracy fragment ion selection to improve glycopeptide detection by precursor ion scanning.

Glycosylation is the most widespread protein modification and is known to modulate signal transduction and several biologically important interactions. In order to understand and evaluate the biological role of glycosylation it is important to identify the glycosylated protein and localize the site glycosylation under particular biological conditions. To identify glycosylated peptides from simple mixtures, i.e., in-gel digests from single SDS PAGE bands we performed high resolution, high accuracy precursor ion scanning using a quadrupole TOF instrument equipped with the Q(2) pulsing function. The high resolving power of the quadrupole TOF instrument results in the selective detection of glycan specific fragment ions minimizing the interference of peptide derived fragment ions with the same nominal mass. Precursor ion scanning has been previously described for these glycan derived ions. However the use of this method has been limited by the low specificity of the method. The analysis using precursor ion scanning can be applied to any peptide mixture from a protein digest without having previous knowledge of the glycosylation of the protein. In addition to the low femtomole (nanomolar) detection limits, this method has the advantage that no prior derivatization or enzymatic treatment of the peptide mixtures is required.

Amino Acid Sequence↗
PubMed1988

Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data.

An implementation of the variable-target-function procedure, first introduced by Braun and Go [W. Braun and N. Go, J. Mol. Biol. 186, 611-626 (1985)], has been used to generate conformations of the small protein bovine pancreatic trypsin inhibitor (BPTI), given a limited set of simulated data that could be obtained by nuclear magnetic resonance (NMR) techniques. A hybrid strategy was also used to calculate conformations of BPTI, given the same information. In the hybrid strategy, low-energy structures of medium-size fragments (decapeptides) of BPTI were generated using the variable-target-function method, followed by restrained energy optimization. The low-energy conformations were used as a basis to build up the complete fifty-eight-residue BPTI molecule. By using the variable-target-function approach, in which energy considerations were not introduced until full conformations of the entire BPTI molecule had been generated, it was not possible to obtain calculated structures with rms deviations from the X-ray conformation of less than 1.6 A for the alpha-carbons. On the other hand, with the hybrid strategy, which involved the consideration of realistic energy terms in the early stages of the calculations, it was possible to calculate low-energy conformations of BPTI with rms deviations from the X-ray structure of 1.06 to 1.50 A for the alpha-carbons. When the rms deviations were computed along the amino acid sequence, it was found that there was a good correlation between deviations among the calculated structures and deviations from the X-ray structure.

Aprotinin↗