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PubMed2005

A calculation of the rovibronic energies and spectrum of the B1A1 electronic state of SiH2.

The B1A1 electronic state of silylene (SiH2) is the second excited singlet state of the molecule and, like the analogous c state of methylene (CH2), it is quasilinear with symmetry 1sigmag+ at linearity. This state dissociates to Si(1D) + H2(1sigmag+). At equilibrium, the B state of SiH2 has an energy that we calculate to be 0.71 eV above that of the dissociation products. However, there is a barrier to dissociation that allows quasibound rovibrational levels to occur, and some have been observed recently [Y. Muramoto et al., J. Chem. Phys. 122, 154302 (2005)]. Starting with our analytical ab initio potential-energy surface, we adjusted it in a fitting to the experimental term values in order to determine the optimum potential-energy function in the bound region. This potential has a C2v equilibrium structure with a SiH bond length of 1.459 angstroms and a bond angle of 165.4 degrees; the barrier to linearity is only 129 cm(-1). Using the optimized potential-energy surface we calculate B-state term values, and using our calculated y and z dipole moment surfaces, we simulate the rotation-vibration spectrum of the state in order to assist in the detection of the matrix isolation spectrum.

Journal Article↗
PubMed1994

Bone remodeling and structural optimization.

Bone remodeling has been viewed both as a process which adapts bone tissue to the mechanical environment at each point in the structure, and as a process which optimally adjusts the tissue distribution within bones to bear the loads placed on them. We have developed a connection between these two views of bone remodeling, in a restricted sense. We start with a remodeling rate equation based on strain energy density. We then define an indicator function which is a weighted sum of total strain energy and a measure of bone mass, and we show that finding bone density distributions in which the remodeling rate equation predicts no changes with time is the same as finding density distributions in which the indicator function is insensitive to small changes in density. The set point in the remodeling rate equation corresponds to a parameter in the indicator function which determines the relative importance of bone mass and strain energy in the optimization indicator function. We have not assessed whether the density distributions which make the density rate of change zero are actually local or global minima for the indicator function in this study, but a related study shows that there is a single unique minimum for the indicator function developed here, implying that a unique solution exists for the bone remodeling rate equations considered in this study.

Biomechanical Phenomena↗
PubMed1988

[Estimation of the energy needs at the national level: use of the FAO/WHO/UNU 1985 approach].

This paper analyzes the methodology proposed by FAO/WHO/UNU 1985 to determine energy requirements and recommendations for population groups. The physiological basis for individual requirements and the components to estimate the energy expenditure of population groups, are presented. This new approach requires a detailed knowledge of the distribution of the population by sex, age and level of physical activity. In the absence of physical activity data the distribution by employment category may be used. Our study suggests characterizing the population through the use of biotypes, according to sex, age and level of physical activity. This new approach also requires the knowledge of weight and height of a representative sample of the population. The planner should also consider a desirable level of physical activity for the population, and decide if the energy recommendation should optimize the weight and height of individuals to promote improved physical well being and health status. The application of this approach to a specific country in Latin America revealed that the available data are insufficient for an adequate estimation of energy needs of the population. Nevertheless, results suggest that the energy gaps for urban sedentary groups are less than those calculated using the traditional FAO/WHO 1973 reference pattern. The energy needs of the countries in the Region will increase as the infant population improves physical development more in accordance with the full expression of their genetic endowment. Further increases in energy needs are estimated as the general population increases the level of discretionary physical activity.

Activities of Daily Living↗
PubMed2002

Development of a laser-induced cell lysis system.

A novel cell lysis system was developed that is based on laser-induced disruption of bacterial and yeast cells. It will find application as a rapid, efficient and clean sample preparation step in bioanalytical detection systems. Using E. coli as our model analyte, we optimized cell lysis with respect to optimal laser wavelength, lowest energy input requirements, RNA release from the cells, and potential protein damage. The optimized system was finally applied to the lysis of four additional microorganisms. All experiments were carried out with about 2000 cells per sample or less. Initially, lysis was determined by the detection of cell survival after laser treatment using standard microbiological techniques, (i.e., cells were grown on nutrient agar plates). Then, actual release of mRNA from the cells was proven. Wavelengths investigated ranged from 500 nm to 1550 nm. An average power of 100 mW for the lasers was shown to be sufficient to obtain cell lysis at wavelengths above 1000 nm, with optimal wavelengths between 1250 nm and 1550 nm. Since water absorbs energy at those wavelengths, it is assumed that laser exposure results in an instantaneous increase of the cell temperature, which causes rupture of the cell membrane. Second, damage to protein solutions treated under optimized laser-lysis conditions was also studied. Using a pure solution of horseradish peroxidase as a model protein, no loss in enzyme activity was observed. Thus, it was concluded that damage to intracellular proteins is unlikely. Third, RNA release was tested using an E. coli specific RNA biosensor. Release of RNA was not detected from untreated cells, but laser-treated E. coli cells displayed significant RNA release due to laser-induced cell lysis. Finally, lysis of M. luteus, B. subtilis, B. cereus, and S. cerevisiae were investigated under optimized conditions. In all cases, laser-induced lysis of the cells was confirmed by determination of cell survival. Hence, laser-induced cell lysis is an efficient procedure that can be used for sample preparation, without damage to macromolecules, in bioanalytical detection systems for microorganisms. Miniaturized lasers and miniaturized cell-lysis chambers will create a simple, field-usable cell lysis system and allow the application of laser-induced cell lysis in micro Total Analysis Systems.

Bacillus cereus↗
PubMed1997

Optimization of spectroscopic and electrophoretic properties of energy transfer primers.

We have synthesized and characterized the spectroscopic properties of 56 energy transfer (ET) fluorescent dye-labeled primers differing in (i) the spacing between the donor and acceptor, (ii) the nature of the spacer (either oligonucleotide or polydideoxyribose phosphate), (iii) the primer sequence (M13 (-40), M13 (-21), M13 reverse, SP6, T3, and T7 priming sequences), and (iv) the dyes chosen as the donor (6-carboxyfluorescein, F; or 3-(epsilon-carboxypentyl)-3'-ethyl-5,5'-dimethyloxacarbocyanine, C) and acceptor (F; 5 & 6-carboxyrhodamine-110, R110; 6-carboxyrhodamine-6G, G; N,N,N',N'-tetramethyl-6-carboxyrhodamine, T; and 6-carboxy-X-rhodamine, R) chromophores. This study led to the development of two significantly improved ET primer sets for multiple-color analyses. These primers are named using the convention D-N-A, where D is the donor, A is the acceptor, and N is the number of nucleotides between the donor and the acceptor. The primer set C4R110, C4G, C4T, and C4R provides acceptor emissions of high spectral purity with donor:acceptor emission ratios of < 0.002 for C4G, < 0.004 for C4T, and < 0.005 for C4R and excellent matching in the electrophoretic mobilities of single-base extension DNA fragments. The C4R110, C4G, C4T, and C4R set is valuable for diagnostic applications where minimization of crosstalk between different labels is of particular importance. The set C10R110, C10G, C10T, and C10R, which uses only rhodamine dyes as acceptors, shows significantly improved matching in the electrophoretic mobilities of single-base extension DNA fragments over the previously described set C10F, C10G, C10T, and C10R and is the best available for sequencing.

DNA↗
PubMed2000

Spatial determination of elements in green leaves of oak trees (Quercus robur) by laser ablation-ICP-MS.

Laser ablation inductively coupled plasma mass spectrometry (laser ablation-ICP-MS) has been applied to the spatially resolved determination of the elements Mg, Ca, Cu, Ni, Ba, Al, Pb, Sr and Mn in green leaves of oak trees. Instrument operating parameters such as the laser wavelength and the pulse energy have been optimized to provide the sensitivity and reproducibility required for the analysis. The method provides spatial resolution down to 300 microm with the use of the 355 nm wavelength (3rd harmonic of the 1,064 nm Nd:YAG laser wavelength) and the pulse energy of 50 mJ. Plant standards and cellulose, doped with multi element solution standards, dried and pressed to pellets were used as calibration samples. To compensate for signal fluctuations caused by the variation of the ablated sample mass 13C was used as a "natural" internal standard. The accuracy of the calibration was verified with selected samples analyzed by ICP-MS (high pressure digestion, 170 degrees C, 10(7) Pa, HNO3, 2 h) and by laser ablation-ICP-MS. Recovery rates between 93% (Cu) and 108% (Mn) were obtained. Leaves taken from oak trees (Quercus robur) were analyzed.

Calibration↗
PubMed1979

The global energy system.

A global energy system is conceptualized and analyzed, the energy distributor sub-system of the worldwide supranational system. Its many interconnections are examined and traced back to their source to determine the major elements of this global energy system. Long-term trends are emphasized. The analysis begins with a discussion of the local systems that resulted from the deployment of technology in the mid-nineteenth century, continues with a description of the global system based on oil that has existed for the past two decades, and ends with a scenario implying that an energy transition will occur in the future in which use of coal, nuclear, and solar energy will predominate. A major problem for the future will be the management of this energy transition. The optimal use of global resources and the efficient management of this transition will require a stable and persistent global order.

Conservation of Natural Resources↗
PubMed1991

[Q-switched Nd:YAG laser surgery on vitreous traction bands].

The Q-switched Nd: YAG laser was used to cut vitreous traction bands in 20 eyes with an effective rate of 85%. The pulse energy ranged from 2.8-8.7mJ, and the total energy required was 196 +/- 155.3mJ. The distance of the laser beam focus to retinal surface was 3.7 +/- 2mm. Nd: YAG vitreolysis is an effective means in releasing traction bands and membranes in the posterior segment of the eye. Adaptation of a proper contact lens and optimal strength of energy with accurate focussing are conducive to increased efficacy and avoidance of retinal injury.

Adolescent↗
PubMed2003

Influence of scatter reduction method and monochromatic beams on image quality and dose in mammography.

In mammography, the image contrast and dose delivered to the patient are determined by the x-ray spectrum and the scatter to primary ratio S/P. Thus the quality of the mammographic procedure is highly dependent on the choice of anode and filter material and on the method used to reduce the amount of scattered radiation reaching the detector. Synchrotron radiation is a useful tool to study the effect of beam energy on the optimization of the mammographic process because it delivers a high flux of monochromatic photons. Moreover, because the beam is naturally flat collimated in one direction, a slot can be used instead of a grid for scatter reduction. We have measured the ratio S/P and the transmission factors for grids and slots for monoenergetic synchrotron radiation. In this way the effect of beam energy and scatter rejection method were separated, and their respective importance for image quality and dose analyzed. Our results show that conventional mammographic spectra are not far from optimum and that the use of a slot instead of a grid has an important effect on the optimization of the mammographic process. We propose a simple numerical model to quantify this effect.

Computer Simulation↗
PubMed2006

Multipass membrane protein structure prediction using Rosetta.

We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures. The membrane environment is modeled by embedding the protein chain into a model membrane represented by parallel planes defining hydrophobic, interface, and polar membrane layers for each energy evaluation. The optimal embedding is determined by maximizing the exposure of surface hydrophobic residues within the membrane and minimizing hydrophobic exposure outside of the membrane. Protein conformations are built up using the Rosetta fragment assembly method and evaluated using a new membrane-specific version of the Rosetta low-resolution energy function in which residue-residue and residue-environment interactions are functions of the membrane layer in addition to amino acid identity, distance, and density. We find that lower energy and more native-like structures are achieved by sequential addition of helices to a growing chain, which may mimic some aspects of helical protein biogenesis after translocation, rather than folding the whole chain simultaneously as in the Rosetta soluble protein prediction method. In tests on 12 membrane proteins for which the structure is known, between 51 and 145 residues were predicted with root-mean-square deviation <4 A from the native structure.

Enzymes↗
PubMed2005

Optimization of brain conformal mapping with landmarks.

To compare and integrate brain data, data from multiple subjects are typically mapped into a canonical space. One method to do this is to conformally map cortical surfaces to the sphere. It is well known that any genus zero Riemann surface can be conformally mapped to a sphere. Therefore, conformal mapping offers a convenient method to parameterize cortical surfaces without angular distortion, generating an orthogonal grid on the cortex that locally preserves the metric. To compare cortical surfaces more effectively, it is advantageous to adjust the conformal parameterizations to match consistent anatomical features across subjects. This matching of cortical patterns improves the alignment of data across subjects, although it is more challenging to create a consistent conformal (orthogonal) parameterization of anatomy across subjects when landmarks are constrained to lie at specific locations in the spherical parameter space. Here we propose a new method, based on a new energy functional, to optimize the conformal parameterization of cortical surfaces by using landmarks. Experimental results on a dataset of 40 brain hemispheres showed that the landmark mismatch energy can be greatly reduced while effectively preserving conformality. The key advantage of this conformal parameterization approach is that any local adjustments of the mapping to match landmarks do not affect the conformality of the mapping significantly. We also examined how the parameterization changes with different weighting factors. As expected, the landmark matching error can be reduced if it is more heavily penalized, but conformality is progressively reduced.

Adult↗
PubMed2005

Endovenous laser ablation of varicose veins.

UNLABELLED: Readily available non-invasive diagnostic tests now allow physicians to accurately map out abnormal venous pathways and identify all sources of reflux. Minimally invasive alternatives to surgical removal of incompetent truncal veins have been developed with impressive RESULTS: Endovenous laser treatment can be performed in the office under local anesthesia and is associated with virtually no recovery period. Better understanding of the primary mechanism of energy transfer by direct contact between the laser fiber tip and vein wall has underscored the importance of vein emptying. Improved utilization of tumescent anesthesia has helped facilitate circumferential laser fiber to vein wall contact and virtually eliminated the incidence of heat-related complications. Further refinements in the technique and optimization of laser energy parameters have improved success rates of vein closure from 90% to nearly 100%. Compared to surgery, endovenous laser has also demonstrated lower rates of recurrence largely due to the absence of neovascularity. This review of endovenous laser treatment should validate this exciting technique as a scientifically acceptable option for eliminating truncal vein reflux. If measured by patient acceptance and satisfaction, endovenous laser and other minimally invasive methods have already supplanted traditional surgery as the treatment of choice for superficial venous insufficiency.

Angioscopy↗
PubMed2006

Unifying constructal theory for scale effects in running, swimming and flying.

Biologists have treated the view that fundamental differences exist between running, flying and swimming as evident, because the forms of locomotion and the animals are so different: limbs and wings vs body undulations, neutrally buoyant vs weighted bodies, etc. Here we show that all forms of locomotion can be described by a single physics theory. The theory is an invocation of the principle that flow systems evolve in such a way that they destroy minimum useful energy (exergy, food). This optimization approach delivers in surprisingly direct fashion the observed relations between speed and body mass (M(b)) raised to 1/6, and between frequency (stride, flapping) and M(b)(-1/6), and shows why these relations hold for running, flying and swimming. Animal locomotion is an optimized two-step intermittency: an optimal balance is achieved between the vertical loss of useful energy (lifting the body weight, which later drops), and the horizontal loss caused by friction against the surrounding medium. The theory predicts additional features of animal design: the Strouhal number constant, which holds for running as well as flying and swimming, the proportionality between force output and mass in animal motors, and the fact that undulating swimming and flapping flight occur only if the body Reynolds number exceeds approximately 30. This theory, and the general body of work known as constructal theory, together now show that animal movement (running, flying, swimming) and fluid eddy movement (turbulent structure) are both forms of optimized intermittent movement.

Animals↗
PubMed1990

High energy (42-66 MeV reactions) fast neutron dose optimization studies in the head and neck, thorax, upper abdomen, pelvis and extremities.

Five hundred and fifty patients were entered into a set of dose-searching studies designed to determine normal tissue tolerance to high energy (42-66 MeV reactions) fast neutrons delivered in 12 equal fractions over 4 weeks. Participating institutions included: The Fermilab (66 MeV p+----Be), The University of Washington (50 MeVp+----Be), U.C.L.A. (45 MeVH-----Be), M.D. Anderson Hospital (42 MeVH-----Be), and The Cleveland Clinic (42 MeVp+----Be). Patients were stratified by treatment facility and then randomized to receive 16, 18 or 20 Gy for tumors located in the upper abdomen or pelvis, and 18, 20 or 22 Gy for tumors located in the head and neck, thorax or extremities. Following completion of the randomized protocols, additional patients were studied at the 20.4 Gy level in the head and neck, thorax and pelvis. Normal tissue effect scoring was accomplished using the RTOG-EORTC acute and late normal tissue effect scales. Acute Grade 3 + toxicity rates in the head and neck were 19% for 20/20.4 Gy and 20% for 22 Gy. Time adjusted late toxicity rates in the head and neck at 12 months were 15% for 20/20.4 Gy and 0% for 22 Gy. The 18 Gy treatment arm of the head and neck protocol was dropped early in the study after only two patients were accrued. For cases treated in the thorax, acute Grade 3 + toxicity rates were 6% for 18 Gy, 15% for 20/20.4 Gy and 7% for 22 Gy. Late toxicity rates at 12 months were 0% for 18 Gy, 11% for 20/20.4 Gy and 18% for 22 Gy. Acute Grade 3+ toxicity rates in the upper abdomen were 0% for 16 Gy, 8% for 18 Gy and 12% for 20 Gy. There were no Grade 3 + late toxicities in the upper abdomen. In the pelvis, acute Grade 3 + toxicity rates were 0% for 16 Gy, 3% for 18 Gy and 3% for 20/20.4 Gy. Late Grade 3 + toxicities at 24 months were 20% for 16 Gy, 5% for 18 Gy and 24% for 20/20.4 Gy. In extremities, acute Grade 3 + toxicity rates were 7% for 20 Gy and 21% for 22 Gy while at 12 months, late Grade 3 + toxicity rates were 14 and 35%, respectively. The 18 Gy treatment arm of the extremities protocol was dropped early in the study after only two patients were accrued. Factors associated with normal tissue effects in addition to treatment dose are discussed.

Abdominal Neoplasms↗
PubMed1992

Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology.

An unknown protein structure can be predicted with fair accuracy once an evolutionary connection at the sequence level has been made to a protein of known 3-D structure. In model building by homology, one typically starts with a backbone framework, rebuilds new loop regions, and replaces nonconserved side chains. Here, we use an extremely efficient Monte Carlo algorithm in rotamer space with simulated annealing and simple potential energy functions to optimize the packing of side chains on given backbone models. Optimized models are generated within minutes on a workstation, with reasonable accuracy (average of 81% side chain chi 1 dihedral angles correct in the cores of proteins determined at better than 2.5 A resolution). As expected, the quality of the models decreases with decreasing accuracy of backbone coordinates. If the back-bone was taken from a homologous rather than the same protein, about 70% side chain chi 1 angles were modeled correctly in the core in a case of strong homology and about 60% in a case of medium homology. The algorithm can be used in automated, fast, and reproducible model building by homology.

Algorithms↗
PubMed1983

[Irradiation of the para-aortic ducts. Presentation of an radiation technic with a largely fixed patient's position].

An irradiation planning program has been developed at the Radiologic University Hospital of Graz which allows an interactive optimization of the energy dose distribution of a Co-60 radiation. This program is running in a minicomputer of type DEC PDP-11/34 under the operation system RSX-11. With the aid of this system, a technique has been developed for irradiating the para-aortic lymph canals which complies with theoretical as well as practical optimization criteria. These optimization criteria are defined, and the usefulness of this irradiation technique is compared with a conventional method and demonstrated on the clinical example.

Aorta↗