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PubMed1991

Conformational space of alpha 1-4 glycosidic linkage: a molecular dynamics study.

Molecular Dynamics simulations have been carried out for 100 ps on crystal structure of beta-cyclodextrin in vacuo and with explicit inclusion of solvent at constant pressure and constant temperature using the GROMOS MD algorithm, with a time step of 0.005 ps. The conformational space of the glycosidic linkage was studied by calculating two virtual dihedrals connecting the successive glucose units for the 2000 structures saved during the two simulations. Three preferred regions for alpha 1-4 glycosidic linkage were found in both the simulations. The use of these virtual dihedral angles in representing the glycosidic linkage is also brought out from these studies.

Algorithms↗
PubMedDate not supplied

Analysis and modeling of information flow and distributed expertise in space-related operations.

Evolving space operations requirements and mission planning for long-duration expeditions require detailed examinations and evaluations of information flow dynamics, knowledge-sharing processes, and information technology use in distributed expert networks. This paper describes the work conducted with flight controllers in the Mission Control Center (MCC) of NASA's Johnson Space Center. This MCC work describes the behavior of experts in a distributed supervisory coordination framework, which extends supervisory control/command and control models of human task performance. Findings from this work are helping to develop analysis techniques, information architectures, and system simulation capabilities for knowledge sharing in an expert community. These findings are being applied to improve knowledge-sharing processes applied to a research program in advanced life support for long-duration space flight. Additional simulation work is being developed to create interoperating modules of information flow and novice/expert behavior patterns.

Communication↗
PubMed1996

Cortico-adrenal function under simulated weightlessness during gestation in the rat--effects on fetal development.

To examine the effects of simulated weightlessness on cortico-adrenal function and on fetal development, we suspended pregnant rats for 20 days. The levels of adrenal and plasma corticosterone were examined in mothers and in fetuses. The animal control group was kept single in standard cages. Growth of the suspended animals was repressed for the first 8 days of the experiment, but thereafter it increased greatly, as did the daily food intake. By the 18th day of the experiment, the body masses and food intake of the two groups were equal. No modification in circulating corticosterone was found. It appears that there is no stress in pregnant rats submitted to simulated weightlessness.

Adaptation, Physiological↗
PubMed1999

Fine-needle aspiration cytologic features of pseudovascular adenoid squamous-cell carcinoma of the lung.

Pseudovascular adenoid squamous-cell carcinoma (PASCC) is an epithelial malignancy with spindle-cell features that can mimic vascular neoplasms, particularly angiosarcoma, in its morphologic characteristics. There have been only a few surgical pathology reports of PASCC arising in the lung, skin, and breast. We describe the fine-needle aspiration (FNA) cytologic and histologic features of a pulmonary PASCC in a 66-yr-old man. The aspiration yielded individually scattered and syncytial fragments of malignant epithelioid-appearing cells with oval to spindle shapes, prominent nucleoli, and a finely vacuolated amphophilic cytoplasm. The core needle biopsy specimen displayed these same cells lining pseudoluminal spaces, with intervening bundles of fibroconnective tissue simulating a vascular neoplasm. The neoplastic cells stained positively with cytokeratin (AE-1/3), epithelial membrane antigen, and vimentin and were nonreactive with S-100, muscle-specific actin, CD31, CD34, and carcinoembryonic antigen. These cytologic, histologic, and immunocytochemical features supported a diagnosis of PASCC. To the best of our knowledge, this is the first report of the FNA cytologic features of this pseudovascular variant of adenoid squamous-cell carcinoma. This FNA case illustrates that the cytologic impression was more accurate and, in fact, that the histologic features of PASCC can be misleading. The correct identification of PASCC and its distinction from angiosarcoma has important clinical ramifications for treatment and prognosis. FNA cytologic examination with ancillary studies is a minimally invasive procedure that can distinguish PASCC from sarcomatous lesions. Diagn. Cytopathol. 1999;21:265-270.

Aged↗
PubMed2002

High-affinity GABA uptake in retinal glial (Müller) cells of the guinea pig: electrophysiological characterization, immunohistochemical localization, and modeling of efficiency.

Glial cells may act as important modulators of neuronal information processing, in particular, via fast uptake of neuronally released transmitters. Here, we characterize the electrogenic gamma-aminobutyric acid (GABA) transporters present in the plasma membranes of Müller (glial) cells of the guinea pig retina and present an estimate of their functional efficiency. The GABA-evoked whole-cell currents are voltage-dependent, with increasing amplitudes and decreasing affinity constants at more negative membrane potentials. The transmembranal GABA transport is concentration-dependent, with near-maximal currents at 100 microM GABA, and is dependent on extracellular sodium and chloride ions; the stoichiometry is 1 GABA/2 Na(+)/1 Cl(-). Immunohistochemical labeling and whole-cell voltage-clamp records reveal that Müller cells express both GAT-1 and GAT-3 (but not GAT-2), and that the transporter proteins are expressed predominantly at plasma membrane sites that, in situ, are localized in the outer retina where GABA uptake is performed exclusively by Müller cells. When extracellular GABA enters the cell interior, it evokes, via activation of the GABA transaminase, an NAD(P)H fluorescence signal selectively in the distal region of the Müller cells where their mitochondria are located. Using our experimental data, we simulated the GABA clearance from the extracellular space surrounding one Müller cell; these estimates show that a pulse of 100 microM extracellular GABA is fully cleared after 70 ms. It is suggested that Müller cells may be involved in the regulation of GABAergic transmission within the retina by providing a fast termination of GABAergic signaling via their highly efficient GABA uptake.

Action Potentials↗
PubMed1995

The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution.

The D-alanyl-D-alanine peptidase from Streptomyces sp. R61 is a 37,500 dalton exocellular enzyme that has served as a model for membrane-bound peptidases that are involved in bacterial cell wall biosynthesis. Inhibition of these enzymes by beta-lactam antibiotics ultimately leads to bacterial cell death. The X-ray crystal structure of the R61 D-alanyl-D-alanine peptidase has been solved using multiple isomorphous replacement, simulated annealing and least squares refinement. The space group and unit cell parameters are P2(1)2(1)2(1) with a = 51.1 A, b = 67.3 A and c = 102.4 A. The structure has been refined using 2 sigma data to 1.6 A resolution with a crystallographic R-factor of 0.148. The model contains 347 residues (2938 atoms) and 254 solvent molecules. The overall temperature factor is 9.6 A2, and the estimated coordinate error is 0.14 A. The protein consists of a single polypeptide chain organized into two regions. One region contains a nine-stranded antiparallel beta-sheet with helices on both faces; this region includes both the amino and carboxyl termini. The second region is all helical. Sixty percent of the residues occur in helices or beta-sheet. The reactive Ser62 is found between the two regions of the enzyme at the amino end of the protein's longest-helix which begins with one turn of 3(10) helix and continues with four turns of alpha-helix. The active site is an elongated pocket that contains four basic and four aromatic residues. An oxyanion hole is formed by Ser62 NH and Thr301 NH. The pocket also contains the few key residues that are conserved in all penicillin-binding proteins and beta-lactamases. Two of these residues, Lys65 and Tyr159, are among the 16 side-chains that take on multiple conformations in the R61 crystal structure. Three of the 12 proline rings adopt two conformations which we believe has not been previously reported. There is no anionic acid equivalent to the catalytic Glu166 found in Class A beta-lactamases. Two ordered water molecules (O507 and O644) are found buried in the active site and hydrogen-bonded to each other (2.6 A). O507 could potentially act as the hydrolytic water molecule for deacylation.

Binding Sites↗
PubMed2002

Glycolysis and oxidative phosphorylation as a function of cytosolic phosphorylation state and power output of the muscle cell.

A mathematical description of the regulation of ATP production in muscle cells is presented whereby the activity of OxP can be calculated as a function of (1) free [ADP] as the substrate and (2) a second driving force PhiDelta G (kilojoules per mole) resulting from the difference of free energy Delta G(ox,ap) (kilojoules per mole)-Delta G(ATP,cyt) (kilojoules per mole). In turn, the term Delta G(ox,ap) results from the proton motive force and the generation of ATP in the matrix space including the ATP-ADP exchange, whereas the phosphorylation state of the CHEP-sytem is described by Delta G(ATP,cyt). Regulation of glycolysis is calculated as a function of free [ADP] and [AMP] at the level of PFK. The PFK is inhibited by a decreasing pH resulting from lactate accumulation. The ATP/PCr equilibrium of the CHEP-system is calculated by algebraic equations. The dynamic behaviour of the metabolic control of ATP production as a function of ATP consumption is calculated by a system of two 1st-order non-linear differential equations, including a time delay considering oxygen transport. Lactate distribution and elimination is calculated using a two-compartment model with an active lactate producing, and a passive, space including lactate elimination by combustion. The simulation of the dynamics of energy metabolism of muscle cells is performed by the stepwise solution of the differential equations with a 5th-order Runge-Kutta-Fehlberg-routine. Examples of various applications of the simulation of the dynamics of energy supply demonstrate the qualitative and quantitative congruence to the behaviour of metabolic processes in experiments during rest, exercise and recovery.

Animals↗
PubMed1990

A model for evaluation of gas exchange: mouth to mouth ventilation of infants by emergency medical technicians.

We describe a model for evaluating techniques of infant ventilation during resuscitation. The utility of the model is illustrated by testing performance of emergency medical technicians in mouth to mouth ventilation of a model 4 kg infant. Ventilation was generally adequate with mean (+/- S.D.) frequency 22 +/- 9 breaths per minute and tidal volume 40 +/- 13 ml. Gas delivered to the model consisted of PICO2 7 +/- 6 mmHg and FIO2 0.20 +/- 0.007. Assuming normal metabolic rate and respiratory dead space, alveolar gas composition resulting from the simulated resuscitations would be PACO2 = 31 +/- 20 and PAO2 = 110 +/- 19 mmHg. Nine of ten rescuers would have achieved satisfactory PACO2 less than or equal to 50 and PAO2 greater than or equal to 100. However, the rescuers' exhaled oxygen concentration is not adequate to correct hypoxemia if associated with hypoventilation or a wide alveolar to arterial oxygen gradient.

Emergencies↗
PubMed2006

Contaminant mass discharge estimation in groundwater based on multi-level point measurements: a numerical evaluation of expected errors.

Different methods for the field-scale estimation of contaminant mass discharge in groundwater at control planes based on multi-level well data are numerically analysed for the expected estimation error. We consider "direct" methods based on time-integrated measuring of mass flux, as well as "indirect" methods, where estimates are derived from concentration measurements. The appropriateness of the methods is evaluated by means of modelled data provided by simulation of mass transport in a three-dimensional model domain. Uncertain heterogeneous aquifer conditions are addressed by means of Monte-Carlo simulations with aquifer conductivity as a random space function. We investigate extensively the role of the interplay between the spatial resolution of the sampling grid and aquifer heterogeneity with respect to the accuracy of the mass discharge estimation. It is shown that estimation errors can be reduced only if spatial sampling intervals are in due proportion to spatial correlation length scales. The ranking of the methods with regard to estimation error is shown to be heavily dependent on both the given sampling resolution and prevailing aquifer heterogeneity. Regarding the "indirect" estimation methods, we demonstrate the great importance of a consistent averaging of the parameters used for the discharge estimation.

Data Collection↗
PubMed2000

Unexpected renal responses in space.

Urine output in astronauts following ingestion of an oral water load was low in space on the Russian space station Mir and less than during simulation by 6 degrees head-down bed rest. This surprising observation shows that the effects of gravity and weightlessness on fluid volume regulation are not well understood and that the head-down bed-rest model does not simulate the effects of weightlessness on renal water handling.

Adult↗
PubMed2000

Calcium binding constituents of the organic shell matrix from the freshwater snail Biomphalaria glabrata.

The Ca2+ binding of an EDTA-free water-soluble (SM) and -insoluble (IM) organic matrix of the freshwater snail Biomphalaria glabrata was investigated, using a 45Ca2+ autoradiography after SDS-electrophoretical separation and a calcium binding assay. Electrophoresis of the SM showed a considerable amount of Alcian blue and Stains all positive material, regarded as glycosaminoglycans (GAGs) or proteoglycans (PGs). This part of the SM was slightly positive after 45Ca2+ autoradiography at pH 6.8. The Ca2+ binding increased, raising the pH to 7.4 and 8.0 and was especially strong when simulating the real conditions of the extrapallial space with a carbonate buffer of pH 7.4. The Ca2+ binding assay of the IM showed the same pH-dependency that was observed in the SM. The titration of the IM with Ca2+ at pH 8.0 lead to a dissociation constant of 7.5 x 10(-5) M. While Mg2+ displaced 45Ca2+ in the same way as nonradioactive Ca2+, an approximately 400-fold amount of Na+ was necessary to reduce the binding of 45Ca2+ to 50%. The Ca2+ binding of the organic matrix from the B. glabrata shell appears to be a process of low specificity, medium affinity and high pH-dependency. Apparently, acidic carbohydrate-rich PGs are the only calcium binding constituents of the organic shell matrix.

Animals↗
PubMed2001

Dose effects of guide wires for catheter-based intravascular brachytherapy.

PURPOSE: Guide wires with high torquability and steerability are commonly used to navigate through a tortuous and/or branching arterial tree in a catheter-based intravascular brachytherapy procedure. The dosimetric effects due to the presence of metallic guide wires have not been addressed. This work investigates these dose effects for the three most commonly used beta and gamma sources (90Sr, 32P, and 192Ir). METHODS AND MATERIALS: The EGS4 Monte Carlo codes were used to calculate the dose distributions for the 90Sr(NOVOSTE), 32P (Guidant), and 192Ir (BEST Ind.) with and without a guide wire in place. Energy spectra for particles exiting the sources were calculated from the full phase-space data obtained from the Monte Carlo simulations of the source constructions. Guide wires of various thicknesses and compositions were studied. RESULTS: The dose perturbations due to the presence of guide wires were found to be far more significant for the 90Sr/90Y and 32P beta sources than those for the 192Ir gamma source. Because of the attenuation by the guide wires, a dose reduction of up to 60% behind a guide wire was observed for the beta sources, whereas the dose perturbation was found to be negligible for the gamma source. For a beta source, the dose perturbations depend on the thickness and the material of the guide wire. When the region behind a guide wire is part of an intravascular brachytherapy target, the presence of the guide wire results in a significant underdosing for beta sources. The underdosed region can extend a few mm behind the guide wire and up to 1 mm in other directions. CONCLUSION: Significant dose perturbations by the presence of a metallic guide wire have been found in catheter-based intravascular brachytherapy using beta sources. The dose effects should be considered in the dose prescription and/or in analyzing the treatment outcome for beta sources. Such precautions are not necessary if using a gamma source.

Beta Particles↗
PubMed2006

Photochemical reactivity of 2-vinylbiphenyl and 2-vinyl-1,3-terphenyl: the balance between nonadiabatic and adiabatic photocyclization.

A mechanism for the photochemical conversion of 2-vinyl-1,3-terphenyl to 8,9a-dihydrophenanthrene (Lewis, F. D.; Zuo, X.; Gevorgyan, V.; Rubin, M. J. Am. Chem. Soc. 2002, 124, 13664-13665) is presented in this study, based on ab initio restricted active space self-consistent field calculations and a molecular mechanics-valence bond dynamics simulation of a model system: the syn isomer of 2-vinylbiphenyl. An extended crossing seam between the ground and first excited electronic states was found to be largely responsible for the efficient photocyclization of the photochemically active syn isomer. This mechanism is nonadiabatic in nature, with an excited-state reaction pathway approaching the crossing region during the initial stage of cyclization. Dynamics simulation shows that this seam is easily accessible by vibrational motion in the branching space, once a small barrier is passed on the S1 excited-state potential energy surface. Ultrafast radiationless decay to the ground state then follows, and the cyclization is completed on this surface. A second possible mechanism was identified, which involves complete adiabatic cyclization on the S1 surface, with decay to the ground state (at a different conical intersection) only taking place once the product is formed. Thus, there is a competition between these two mechanisms-nonadiabatic and adiabatic-governed by the dynamics of the system. A large quantum yield is predicted for the photocyclization of the syn isomer of 2-vinylbiphenyl and 2-vinyl-1,3-terphenyl, in agreement with experimental observations.

Journal Article↗
PubMed2005

Modeling the similarity and divergence of dopamine D2-like receptors and identification of validated ligand-receptor complexes.

Focusing on the similarity and divergence of GPCR subtypes and their ligand interactions, we generated dopamine D2, D3, and D4 receptor models based on the rhodopsin crystal structure and refined these with an extensive MM/MD protocol. After validation by diagnostic experimental data, subtype-specific relative positions of TM1, 2, 6, and 7 and bending angles of TM7 were found. To sample the conformational space of the complex, we performed simulated-annealing runs of the receptor protein with the sub-nanomolar antagonist spiperone. Docking a representative set of ligands, we were able to identify one superior model for each subtype when excellent correlations between predicted energies of binding and experimental affinities (r2 = 0.72 for D2, 0.91 for D3 and 0.77 for D4) could be observed. Further analysis revealed general ligand interactions with ASP3.32 and aromatic residues in TM6/7 and individual key interactions with TM1 and TM2 residues of the D3 and D4 receptor models, respectively.

Amino Acid Sequence↗
PubMed1998

A proposed bioactive conformation of peptide T.

The conformational profiles of Peptide T, (5-8)Peptide T, [Abu5](4-8)Peptide T and (4-8)Peptide T were computed independently to assess the geometrical characteristics of the bioactive conformation of Peptide T. The conformational profiles of the peptides were computed within the molecular mechanics framework using an effective dielectric constant of 80. The conformational space was thoroughly sampled using an iterative simulated annealing protocol. The bioactive conformation was assessed by pairwise cross comparisons of each of the unique low energy conformations found for each of the different analogs studied. After a putative bioactive conformation was selected, in order to further validate our hypothesis the conformational profile of the potent compound cyclo(Thr-Thr-Asn-Tyr-Thr-Asp) was computed and the putative bioactive conformation was found. The conformation exhibits a pseudo beta-turn involving the side chain of Thr5 and the carbonyl oxygen of Tyr7 forming a C12 ring.

Amino Acid Sequence↗
PubMedDate not supplied

Oscillations and irregular emission in networks of linear spiking neurons.

The dynamics of a network of randomly connected inhibitory linear integrate and fire (LIF) neurons (with a floor for the depolarization), in the presence of stochastic external afferent input, is considered in various parameter regimes of the neurons and of the network. Applying a technique recently introduced by Brunel and Hakim, we classify the regimes in which such a network has stable stationary states and in which spike emission rates oscillate. In the vicinity of the bifurcation line, the oscillation frequency and its amplitude are computed and compared with simulations. As for leaky IF neurons, the space of parameters can be compacted into two. Yet despite significant technical differences between the two models, related to both the different dynamics of the depolarization as well as to the different boundary conditions, the qualitative behavior is rather similar. The significance of LIF neurons and of the differences with leaky IF neurons is discussed.

Action Potentials↗
PubMed2005

A new isoreticular class of metal-organic-frameworks with the MIL-88 topology.

We report here a new family of isoreticular MOFs, comprising three larger analogues of the nanoporous metallocarboxylate MIL-88; these solids were synthesized using a controlled SBU approach and the three crystal structures were solved using an original simulation-assisted structure determination method in direct space.

Journal Article↗
PubMed2003

A simple method to test if the internal mammary lymph nodes are covered by the wide tangent technique in radiotherapy for high-risk breast cancer.

AIM: It is often complicated to include the internal mammary lymph nodes in the radiation field after breast-conserving therapy. Using the wide tangent technique the internal mammary lymph nodes are generally presumed to be included if the medial tangential field border is placed 3 cm across the midline. The current study was designed to test the validity of this assumption, and if possible, to correct the wide tangents without using computed tomography (CT) scanning. PATIENTS AND METHODS: Twenty-one consecutive, high-risk, post-lumpectomy patients were included. An arrangement of three copper wires was mounted in wax placed perpendicular to the skin surface at the ipsilateral border of sternum at intercostal spaces 2 to 4. During a standard simulation for wide tangents, it was examined if the length of the copper wires projected beneath the skin surface (representing the depth of the internal mammary lymph nodes, measured by ultrasound) were included in the wide tangent fields. RESULTS: In only one patient were the internal mammary lymph nodes covered by the wide tangent technique. In 14 of the remaining 20 patients the lateral tangential field border was subsequently moved in the posterior direction, and the internal mammary lymph nodes could be included without unacceptable normal tissue involvement. In the last six patients the irradiated heart and lung volumes exceeded acceptable tolerance levels with this correction, and these patients were referred for three-dimensional CT dose planning. CONCLUSION: The presented simple technique may be helpful if CT scanning is not available. In all other cases CT-based dose plan should ideally be used as a standard in the planning of radiotherapy after breast-conserving surgery to assure optimal inclusion of the relevant target, and to avoid irradiation of large volumes of critical normal tissue.

Adult↗