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PubMedDate not supplied

NMR T2 distributions and two phase flow simulations from x-ray micro-tomography images of sandstones.

The distribution of fluids in the pore space of a series of sandstones is calculated as a function of capillary pressure using a two phase flow simulation model. The pore space is represented by a system of channels and nodes which are derived from x-ray micro-tomography images of sandstones. The sandstones studied varied in permeability from approximately 40 to 3,000 mD. The simulation results illustrate the significance of the pore level by-pass phenomena in controlling the location of fluids within the pore structure. The implications of these results on the interpretation of NMR T(2) distributions to determine the irreducible water saturation are discussed.

Computer Simulation↗
PubMed1998

The influence of CO2 in a space-like environment: study design.

For the operation of manned spacecraft, the removal of CO2 from the cabin atmosphere, produced by its inhabitants, is essential. This is accomplished by chemical absorption in a gas processing unit, a process which requires energy and consumables. Therefore, in terms of resource management, the CO2-level should be kept as high as possible. Otherwise, considering crew health and performance and also the interference with life science experiments, the CO2 load should be as on Earth, close to zero. In order to obtain more information about the permissible CO2 level for future space missions and also to clarify Space Station design criteria, NASA-ESA-DARA have initiated a ground-based simulation study with two different CO2 levels: 0.7% (first campaign) and 1.2% CO2 (second campaign). For this study the deep diving facility of DLR was used to provide atmospheric control and long-term habitation for the test subjects in studying the effect of increased CO2 on physiological and psychological functions. A number of experiments were implemented, which tested selected effects of raised CO2 on humans. Four male subjects stayed in the chamber for 26 d in each campaign, in order to perform the different tests in repeated trials, with the aim of evaluating possible long-term effects. CO2 was controlled by absorption with soda lime, flushing with fresh air and the addition of CO2, if necessary. Essentially, the CO2 produced by the subjects was used to maintain the level at 0.7 and 1.2%, respectively. Basic control of CO2 was carried out in the soda lime container of the Life Support System. In order to maintain the required level, the amount of gas flowing through the soda lime could be adjusted by a remote controlled bypass. With this set-up it was possible to keep CO2 at an average level between 0.67 and 0.73% in the first campaign and between 1.17 and 1.23% in the second campaign. The results of the experiments support the current CO2 limits for space operations, insofar as values around 1% do not impose any severe restrictions to human habitation for at least several weeks, whereas life sciences experiments especially sensitive to CO2 influences have to be carefully evaluated for possible interferences.

Adult↗
PubMed2002

Intercalation of cyclic ethers into vanadyl phosphate.

Two cyclic ethers, tetrahydrofuran (THF) and tetrahydropyran (THP), were intercalated into vanadyl phosphate and characterized by X-ray powder diffraction, thermogravimetry, and IR and Raman spectroscopy. Both compounds contain one molecule of ether per formula unit of VOPO(4) and show high thermal stability in comparison with VOPO(4) intercalates with other organic guest molecules. Both ethers are anchored to the VOPO(4) host layers by their oxygen atoms, which are coordinated to the vanadium atoms of the host. The probable arrangement of the tetrahydropyran molecules in the host interlayer space is derived from molecular simulations by the Cerius(2) 4.5 program.

Journal Article↗
PubMed1997

Ideal architecture of residue packing and its observation in protein structures.

A simple model of sphere packing has been investigated as an ideal model for long-range interactions for the packing of non-bonded residues in protein structures. By superposing all residues, the geometry of packing around a central residue is investigated. It is found that all residues conform almost perfectly to this lattice model for sphere packing when a radius of 6.5 A is used to define non-bonded (virtual) interacting residues. Side-chain positions with respect to sequential backbone segments are relatively regular as well. This lattice can readily be used in conformation simulations to reduce the conformational space.

Amino Acids↗
PubMed2002

Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field.

One of the conclusions drawn at the CASP4 meeting in Asilomar was that applying various force fields during refinement of template-based models tends to move predictions in the wrong direction, away from the experimentally determined coordinates. We have derived an all-atom force field aimed at protein and nucleotide optimization in vacuo (NOVA), which has been specifically designed to avoid this problem. NOVA resembles common molecular dynamics force fields but has been automatically parameterized with two major goals: (i) not to make high resolution X-ray structures worse and (ii) to improve homology models built by WHAT IF. Force-field parameters were not required to be physically correct; instead, they were optimized with random Monte Carlo moves in force-field parameter space, each one evaluated by simulated annealing runs of a 50-protein optimization set. Errors inherent to the approximate force-field equation could thus be canceled by errors in force-field parameters. Compared with the optimization set, the force field did equally well on an independent validation set and is shown to move in silico models closer to reality. It can be applied to modeling applications as well as X-ray and NMR structure refinement. A new method to assign force-field parameters based on molecular trees is also presented. A NOVA server is freely accessible at http://www.yasara.com/servers

Algorithms↗
PubMed1986

The effect of hypokinesia and hypodynamia on protein turnover and the growth of four skeletal muscles of the rat.

An animal suspension model has been used to simulate the weightlessness experienced during space travel. This procedure results in a reduction in the normal shortening (i.e. hypokinesia) and force generation functions of hind limb muscles (i.e. hypodynamia). The ensuing muscle atrophy was studied over 12 days in different muscle types. Slow muscles (e.g. the soleus) underwent a more pronounced atrophy than intermediate (i.e. gastrocnemius) and fast phasic muscles (e.g. extensor digitorum longus). In all muscle types inactivity resulted in a smaller accumulation of DNA and losses of RNA and protein after 5 days. The latter arose from a decrease in the rate of protein synthesis (measured in vivo) and an increase in protein breakdown. Increased specific activities of cathepsins B and D also supported the view that there is an increased proteolysis after hypokinesia and hypodynamia. When the inactive soleus was simultaneously held in a lengthened (stretched) state the atrophy was prevented through a large increase in the fractional rate of protein synthesis. Protein degradation remained elevated with stretch, thereby slowing the growth of these muscles relative to those in pair-fed, ambulatory controls. The much smaller atrophy of the tibialis anterior and extensor digitorum longus muscles in suspended only limbs represented an underestimate of the true atrophic effects of hypokinesia and hypodynamia. In this model gravity pulls the suspended foot into a plantar flexed position, thereby permanently stretching and protecting such flexor muscles. When this influence of stretch was removed a greater atrophy ensued, mainly due to the loss of the stretch-induced stimulation of protein synthesis.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1996

Drug delivery to brain tumors.

We develop a macroscopic model for delivering drug to brain tumors. The model accounts for bulk convective and diffusive transport across the blood-brain barrier and through the interstitial space. Through mathematical analysis and simulations, we assess the effects of changing parameters (within physiological bounds) on drug delivery. We find that there is an optimal treatment for convective drug delivery to the center of the tumor. We interpret this phenomenon in terms of traffic flow. The implications of our analyses on existing chemotherapeutic protocols are discussed.

Antineoplastic Agents↗
PubMed1982

Skeletal abnormalities in rats induced by simulated weightlessness.

A hypokinetic model has been developed which attempts to simulate the weightlessness experienced during space flight. Male rats (approximately 130 g) were suspended from the model with a head-down tilt for a two-week period. Total mechanical unloading of the hind limbs and partial unloading of the fore limbs occurred. In comparison to pair-fed control rats, the skeletal alterations in the proximal tibial and humeral metaphyses of suspended rats were determined to be a diminished rate of longitudinal bone growth, a reduced mass of mineralized tissue, and an accumulation of marrow fat. Also, suspended rats exhibited decreased numbers of osteoblasts and increased numbers of osteoclasts immediately adjacent to the growth plate-metaphyseal junction at both skeletal sites. Although the reduction in mineralized tissue and the fat accumulation were more marked in the tibia, the skeletal changes in the proximal tibial and humeral metaphyses were generally comparable. The observed abnormalities may be due to mechanical unloading and/or a hypersecretion of corticosteroids.

Adipose Tissue↗
PubMed1992

A unique structural feature of a phospholipase A2 is probed by molecular dynamics.

The unusual catalytic network, revealed by the crystal structure of one of the two phospholipases A2 (PLA2) from the venom of the crotalid A.p.piscivorus has been probed using molecular dynamics. The catalytic network has been remodeled to a conformation similar to that found in all other PLA2, and the modeled structure has been submitted to energy minimization and molecular dynamics simulation, to explore the conformational space of the network. The calculations have yielded a large reorganization of the catalytic network, which gets a conformation close to that of the crystal structure. These results suggest that the unusual catalytic network observed in the studied PLA2 is a structural feature of the protein and not a crystal artifact.

Amino Acid Sequence↗
PubMed1995

Combined action of optokinetic reflex (OKR) and vestibulo-ocular reflex (VOR) in macaque monkey during transient stimulation.

Interaction of vestibulo-ocular reflex (VOR) and optokinetic reflex (OKR) was studied in macaque monkeys by recording horizontal eye movements during transient rotations of their heads and/or an optokinetic pattern in space. At low peak velocities of the stimuli (1.25 degrees/s, 10.0 degrees/s) the eyes were rather well stabilized on the optokinetic pattern, independently of whether the head, the pattern, or both were rotated. At higher velocities (40.0 degrees/s), the OKR gain was attenuated and, when combining vestibular and optokinetic stimuli, the eyes became increasingly stabilized in space. The data could be simulated by a computer model previously designed to describe VOR-OKR interaction during sinusoidal rotations. In this model eye stabilization primarily relies on the OKR, while the role of the VOR is to compensate for the limited bandwidth of the OKR.

Animals↗
PubMed1987

In vivo and in vitro activity of ciprofloxacin plus azlocillin against 12 streptococcal isolates in a neutropenic site model.

Closed-space neutropenic infection sites were simulated in rabbits by subcutaneous semipermeable chambers that were inoculated with 5 X 10(4) CFU/ml of various strains of Streptococcus pneumoniae, Streptococcus faecalis, and Streptococcus avium. Four hours after inoculation, treatment was begun with ciprofloxacin, 10 or 30 mg/kg, azlocillin, 100 mg/kg, amikacin, 15 mg/kg, procaine penicillin G, 300 U/dose, or gentamicin, 2 mg/kg, alone and in two-drug combinations. Antimicrobials were given intramuscularly every 6 hr for 16 doses. Extravascular chambers were sampled throughout the treatment course for bacterial counts and antimicrobial concentration. In vivo results were compared to in vitro tests of inhibition, killing, and synergism. Ciprofloxacin alone had little effect on the animal infection sites. Azlocillin alone reduced, in vivo, eight of 12 isolates greater than or equal to 5 log10 CFU/ml by 92 hr as compared to control. Azlocillin plus ciprofloxacin reduced all 12 isolates greater than or equal to 5 log10 CFU/ml by 92 hr, whereas amikacin plus azlocillin reduced only three and penicillin plus gentamicin only one of the six group D streptococcal isolates greater than or equal to 5 log10 CFU/ml.

Amikacin↗
PubMed2006

Investigation of two-dimensional acoustic resonant modes in a particle separator.

Within an acoustic standing wave particles experience acoustic radiation forces, a phenomenon which is exploited in particle or cell manipulation devices. When developing such devices, one-dimensional acoustic characteristics corresponding to the transducer(s) are typically of most importance and determine the primary radiation forces acting on the particles. However, radiation forces have also been observed to act in the lateral direction, perpendicular to the primary radiation force, forming striated patterns. These lateral forces are due to lateral variations in the acoustic field influenced by the geometry and materials used in the resonator. The ability to control them would present an advantage where their effect is either detrimental or beneficial to the particle manipulation process. The two-dimensional characteristics of an ultrasonic separator device have been modelled within a finite element analysis (FEA) package. The fluid chamber of the device, within which the standing wave is produced, has a width to height ratio of approximately 30:1 and it is across the height that a half-wavelength standing wave is produced to control particle movement. Two-dimensional modal analyses have calculated resonant frequencies which agree well with both the one-dimensional modelling of the device and experimentally measured frequencies. However, these two-dimensional analyses also reveal that these modes exhibit distinctive periodic variations in the acoustic pressure field across the width of the fluid chamber. Such variations lead to lateral radiation forces forming particle bands (striations) and are indicative of enclosure modes. The striation spacings predicted by the FEA simulations for several modes compare well with those measured experimentally for the ultrasonic particle separator device. It is also shown that device geometry and materials control enclosure modes and therefore the strength and characteristics of lateral radiation forces, suggesting the potential use of FEA in designing for the control of enclosure modes in similar particle manipulator devices.

Journal Article↗
PubMed1991

Case report: unusual CT appearances in a case of Budd-Chiari syndrome.

We describe a case of Budd-Chiari Syndrome due to hepatic venous blockage in which there were multiple space-occupying lesions on CT simulating tumour deposits. Ultrasound directed liver biopsy and laparoscopy proved these to be areas of haemorrhagic necrosis consistent with Budd-Chiari Syndrome without any evidence of malignancy. The CT finding of multiple large focal non-enhancing areas in liver does not always indicate tumour deposits in a patient suspected to have Budd-Chiari Syndrome.

Adult↗
PubMedDate not supplied

Cone contrasts do not predict color constancy.

A successive, asymmetric color-matching paradigm was used to investigate the link between cone contrast and the stability of perceived colors. We measured the perceived color shifts of 10 Munsell samples, induced by test illuminant A, simulated in u'v' color space. The capacity of the visual system to resist these shifts, otherwise known as color constancy, is measured in terms of the Brunswik ratio, BR. Cone contrasts are calculated with respect to either the physical or perceived background. Subjective cone contrasts show a better fit to the von Kries law than those based on the physical background. Complete cone adaptation occurs when color constancy is high. However we show conditions where cone adaptation seems complete but color constancy is poor.

Color↗
PubMed1997

NMR and structural model of dynorphin A (1-17) bound to dodecylphosphocholine micelles.

Dynorphin A (1-17) (dynorphin) acts preferentially and with high affinity at the kappa-opioid receptor, for which it is the natural, endogenous ligand. Interest in designing new ligands to interact at the kappa-opioid receptor is based in part on the desire to circumvent some of the problems associated with mu-opioid ligands such as morphine. The high-resolution structure of dynorphin in an environment which closely resembles its environment in vivo could be considered as an important lead for new drugs. The interactions that occur between dynorphin and a model membrane are potentially important, as peptide hormone activity is thought to be mediated by interactions with the cell membrane. Therefore, we have determined the high-resolution structures of dynorphin in a model membrane. Results from our laboratory have shown the existence of an alpha-helical region in dynorphin from residues Gly3 through Arg9 when bound to perdeuterated dodecylphosphocholine (DPC) micelles. In this report we show that dynorphin is bound to DPC micelles and describe a family of dynorphin structures that is alpha-helical from residues Gly3 through Pro10 and that contains a beta-turn from residues Trp14 through Gln17. A model of interaction with the micelle is also reported and is discussed in the context of hormone action in vivo. The structures were determined with 1D and 2D nuclear magnetic resonance spectroscopy, distance geometry in dihedral angle space, and restrained molecular dynamics simulations.

Amino Acid Sequence↗
PubMedDate not supplied

Production of a sialylated N-linked glycoprotein in insect cells.

Under High Aspect Ratio Vessel (HARV) bioreactor culture conditions designed to simulate the microgravity of orbital space flight, insect tissue culture cells infected with a baculovirus expression vector produced a human glycoprotein with tri- and tetra-antennary complex N-linked oligosaccharides containing terminal sialic acid residues. The oligosaccharide structures were similar to those produced in human placental cells. Insect cells cultured in T-flasks only performed incomplete oligosaccharide processing. The mechanism of HARV-mediated changes in the eukaryotic N-linked glycosylation pathway was investigated and could be mimicked under T-flask growth conditions with the addition of N-acetylmannosamine to the culture medium. The significance of these investigations is discussed with respect to the production of recombinant therapeutic glycoproteins, insect physiology, and orbital space flight.

Animals↗
PubMed2006

Oxygen K-edge X-ray absorption fine structure studies of vacuum-deposited ice films.

Multilayer ice films deposited on polycrystalline Au(111) substrates at 90 and 153 K under ultra-high-vacuum conditions are studied using O K-edge X-ray absorption fine structure spectroscopy in the surface-sensitive partial electron yield mode. Both near-edge and extended oscillatory fine structures are analyzed in combination with the theoretical real-space full-multiple-scattering simulations based on the FEFF8 code. The experimental data consistently indicate that the local structure of the near-surface regions in ice films at both substrate temperatures resembles that of high-density crystalline modifications of ice (e.g., ice II, ice III, or high-density amorphous ice). In addition, the ice films deposited at 153 K most probably contain a minor fraction of low-density cubic ice (I(c) phase).

Journal Article↗
PubMed2000

Leakage along warm gutta-percha fillings in the apical canals of curved roots.

The aim of this study was to investigate the leakage along the apical portion of warm gutta-percha obturated curved canals. Human mandibular premolars with single, curved (21 degrees-40 degrees) canals were prepared using the Lightspeed technique. Two groups of prepared canals, matched according to curvature and prevalence of apical transportation, were obturated by two techniques. Coronal gutta-percha was removed immediately after root obturation was completed to simulate the procedure for post space preparation. Leakage along the apical 3 mm of root filling was measured with a fluid transport device. Vertical condensation of warm gutta-percha and Pulp Canal Sealer provided less leakage than Thermafil plastic obturators and AH26 sealer (P = 0.002).

Bicuspid↗