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PubMed2000

Fourier Transform Spectroscopy of Chemiluminescence from the SrO A(1)Sigma(+)-X(1)Sigma(+) Transition.

The A(1)Sigma(+)-X(1)Sigma(+) chemiluminescence spectrum of SrO was observed using a Fourier transform spectrometer. SrO was produced in a Broida-type oven from the Sr + N(2)O reaction. A total of 75 bands from (88)SrO, (87)SrO, and (86)SrO were measured in the range of 7600-13 600 cm(-1) at a resolution of 0.04 cm(-1). The vibrational levels of the ground state were observed up to v" = 12 and over 10 000 rovibrational lines with J as high as 153 were analyzed at a precision of about 0.005 cm(-1). Significantly improved spectral constants for the ground state were obtained by representing the perturbed excited state by term values and by adding the known microwave data and infrared data to our fit. Strong perturbations were observed in the upper A state. The vibrational levels of the A(1)Sigma(+) state were measured up to v' = 8 and some new perturbations are reported. Copyright 2000 Academic Press.

Journal Article↗
PubMed2004

Regulation of ureteric bud branching morphogenesis by sulfated proteoglycans in the developing kidney.

Glycosaminoglycans in the form of heparan sulfate proteoglycans (HSPG) and chondroitin sulfate proteoglycans (CSPG) are required for normal kidney organogenesis. The specific roles of HSPGs and CSPGs on ureteric bud (UB) branching morphogenesis are unclear, and past reports have obtained differing results. Here we employ in vitro systems, including isolated UB culture, to clarify the roles of HSPGs and CSPGs on this process. Microarray analysis revealed that many proteoglycan core proteins change during kidney development (syndecan-1,2,4, glypican-1,2,3, versican, decorin, biglycan). Moreover, syndecan-1, syndecan-4, glypican-3, and versican are differentially expressed during isolated UB culture, while decorin is dynamically regulated in cultured isolated metanephric mesenchyme (MM). Biochemical analysis indicated that while both heparan sulfate (HS) and chondroitin sulfate (CS) are present, CS accounts for approximately 75% of the glycosaminoglycans (GAG) in the embryonic kidney. Selective perturbation of HS in whole kidney rudiments and in the isolated UB resulted in a significant reduction in the number of UB branch tips, while CS perturbation has much less impressive effects on branching morphogenesis. Disruption of endogenous HS sulfation with chlorate resulted in diminished FGF2 binding and proliferation, which markedly altered kidney area but did not have a statistically significant effect on patterning of the ureteric tree. Furthermore, perturbation of GAGs did not have a detectable effect on FGFR2 expression or epithelial marker localization, suggesting the expression of these molecules is largely independent of HS function. Taken together, the data suggests that nonselective perturbation of HSPG function results in a general proliferation defect; selective perturbation of specific core proteins and/or GAG microstructure may result in branching pattern defects. Despite CS being the major GAG synthesized in the whole developing kidney, it appears to play a lesser role in UB branching; however, CS is likely to be integral to other developmental processes during nephrogenesis, possibly involving the MM. A model is presented of how, together with growth factors, heterogeneity of proteoglycan core proteins and glycosaminoglycan sulfation act as a switching mechanism to regulate different stages of the branching process. In this model, specific growth factor-HSPG combinations play key roles in the transitioning between stages and their maintenance.

Animals↗
PubMed1994

Effect of fiducial marker localization on stereotactic target coordinate calculation in CT slices and radiographs.

Novel methods are presented which allow the estimation of the effect of stereotactic fiducial marker localization on target localization in a stereotactic surgery planning program based on the integration of image data from various modalities. The results of simulations are presented. A method for the evaluation of the effect of fiducial marker localization error on stereotactic localization, both for computed tomography (CT) and digitized radiography. Is proposed based on perturbation studies. For tomographic data, the comparison of the stability of two types of fiducial localizers: a standard commercial device based on nine (six vertical and three oblique) rods and an imaginary system with an extra set of rods, called '4-N', is discussed. Results of the perturbation studies clearly indicate the necessity of sub-pixel registration of the fiducial markers in CT. On the other hand, results demonstrate that stereotactic localization based on projection images is less sensitive to fiducial localization error than CT. Finally, the authors present an algorithm for the localization of fiducial markers to sub-pixel accuracy in radiographs acquired with a commercial angio localizer.

Algorithms↗
PubMed2004

Increased expression of VEGF in retinal pigmented epithelial cells is not sufficient to cause choroidal neovascularization.

Increased expression of vascular endothelial cell growth factor (VEGF) in the retina is sufficient to stimulate sprouting of neovascularization from the deep capillary bed of the retina, but not the superficial retinal capillaries or the choriocapillaris. Coexpression of VEGF and angiopoietin 2 (Ang2) results in sprouting of neovascularization from superficial and deep retinal capillaries, but not the choriocapillaris. However, retina-derived VEGF and Ang2 may not reach the choriocapillaris, because of tight junctions between retinal pigmented epithelial (RPE) cells. To eliminate this possible confounding factor, we used the human vitelliform macular dystrophy 2 (VMD2) promoter, an RPE-specific promoter, combined with the tetracycline-inducible promoter system, to generate double transgenic mice with inducible expression of VEGF in RPE cells. Adult mice with increased expression of VEGF in RPE cells had normal retinas and choroids with no choroidal neovascularization (CNV), but when increased expression of VEGF in RPE cells was combined with subretinal injection of a gutless adenoviral vector containing an expression construct for Ang2 (AGVAng2), CNV consistently occurred. In contrast, triple transgenic mice with induced expression of Ang2 and VEGF in RPE cells, did not develop CNV. These data suggest that increased expression of VEGF and/or Ang2 in RPE cells is not sufficient to cause CNV unless it is combined with a subretinal injection of a gutless adenoviral vector, which is likely to perturb RPE cells. These data also suggest that the effects of angiogenic proteins may vary among vascular beds, even those that are closely related, and, therefore, generalizations should be avoided.

Angiopoietin-2↗
PubMedDate not supplied

[Propagation of perturbations in active media with autooscillatory properties].

Propagation of an activity impulse in the medium where autooscillatory relaxation biochemical reaction takes place is examined theoretically and with the help of the computer experiment. Propagation velocities of the front and shape of the impulse are found. The results are compared with axiomatic theory data on spontaneous activity perturbated media.

Mathematics↗
PubMed2006

Hodgkin-Huxley type ion channel characterization: an improved method of voltage clamp experiment parameter estimation.

The Hodgkin-Huxley formalism for quantitative characterization of ionic channels is widely used in cellular electrophysiological models. Model parameters for these individual channels are determined from voltage clamp experiments and usually involve the assumption that inactivation process occurs on a time scale which is infinitely slow compared to the activation process. This work shows that such an assumption may lead to appreciable errors under certain physiological conditions and proposes a new numerical approach to interpret voltage clamp experiment results. In simulated experimental protocols the new method was shown to exhibit superior accuracy compared to the traditional least squares fitting methods. With noiseless input data the error in gating variables and time constants was less than 1%, whereas the traditional methods generated upwards of 10% error and predicted incorrect gating kinetics. A sensitivity analysis showed that the new method could tolerate up to approximately 15% perturbation in the input data without unstably amplifying error in the solution. This method could also assist in designing more efficient experimental protocols, since all channel parameters (gating variables, time constants and maximum conductance) could be determined from a single voltage step.

Animals↗
PubMed2001

Experimental p(wall) and p(cel) correction factors for ionization chambers in low-energy clinical proton beams.

Current dosimetry protocols for clinical protons using ionization chambers do not take into account ionization chamber-dependent perturbation correction factors. In the present investigation, the relative response of 17 cylindrical ionization chambers was evaluated at three proton beam qualities: at two points in a modulated beam and one point in a non-modulated beam, all with an incident energy of 75 MeV. Thirteen of the ionization chambers had a Farmer-type geometry but consisted of different combinations of wall and central electrode materials. All ionization chambers were calibrated in terms of air kerma as well as in terms of absorbed dose to water in a 60Co beam. The relative response of the ionization chambers was compared with results of Monte Carlo simulations of proton and secondary electron transport in the phantom and the ionization chamber geometry. The results of the measurements for cylindrical ionization chambers show relative perturbation effects that are limited to 0.5-1%, resulting in perturbation correction factors that are larger than unity compared with an NE2571 ionization chamber. The experimental relative wall and total perturbation correction factors agree with Monte Carlo calculated values, indicating that the differences between the responses of different ionization chambers are due to secondary electron effects. This conclusion is supported by the comparison of our results with those from other investigators after re-analysis of their data. The central electrode perturbation correction factor for an aluminium electrode in a Farmer-type geometry was found to be unity within the experimental uncertainties.

Electrons↗
PubMed2006

Perturbation-correlation moving-window two-dimensional correlation spectroscopy.

A new method of analysis, perturbation-correlation moving-window two-dimensional (PCMW2D) correlation spectroscopy, is proposed. For a spectral data set collected under an external perturbation, this method provides a pair of synchronous and asynchronous two-dimensional correlation spectra plotted on a plane between a spectral variable (e.g., wavenumber) axis and a perturbation variable (e.g., temperature) axis. One of the advantages of this new correlation analysis method is that complicated spectral variation along the perturbation direction can be monitored. It has been found that the synchronous and asynchronous PCMW2D correlation spectra are similar to the first perturbation derivative and negative second perturbation derivative spectra of the original data, respectively. To demonstrate the potential of PCMW2D correlation spectroscopy, it has been applied to temperature-dependent infrared (IR) spectra of a poly(vinyl alcohol) (PVA) film. The thermal behavior of the PVA film has been revealed by the PCMW2D correlation analysis. Two characteristic cross-peaks are observed in the synchronous PCMW2D correlation spectra generated from the temperature-dependent IR spectra between the crystalline phase C-O stretching band at 1141 cm-1 and the melting temperature of 209 degrees C and between the amorphous phase C-O stretching band at 1095 cm-1 and another specific temperature of 233 degrees C. This specific temperature of 233 degrees C corresponds to the thermal degradation temperature due to the elimination of the hydroxyl group attached to the main chain.

Journal Article↗
PubMedDate not supplied

Constrained reconstruction: a superresolution, optimal signal-to-noise alternative to the Fourier transform in magnetic resonance imaging.

Many problems in physics involve imaging objects with high spatial frequency content in a limited amount of time. The limitation of available experimental data leads to the infamous problem of diffraction limited data which manifests itself by causing ringing in the image. This ringing is due to the interference phenomena in optics and is known as the Gibbs phenomenon in engineering. Present techniques to cope with this problem include filtering and regularization schemes based on minimum norm or maximum entropy constraints. In this paper, a new technique based on object modeling and estimation is developed to achieve superresolution reconstruction from partial Fourier transform data. The nonlinear parameters of the object model are obtained using the singular value decomposition (SVD)-based all-pole model framework, and the linear parameters are determined using a standard least squares estimation method. This technique is capable, in principle, of unlimited resolution and is robust with respect to Gaussian white noise perturbation to the measured data and with respect to systematic modeling errors. Reconstruction results from simulated data and real magnetic resonance data are presented to illustrate the performance of the proposed method.

Fourier Analysis↗
PubMed1999

Three-dimensional analysis of the 16 nm urothelial plaque particle: luminal surface exposure, preferential head-to-head interaction, and hinge formation.

The luminal surface of mouse urothelium in contact with the urine is almost entirely covered with plaques consisting of uroplakin-containing particles that form p6 hexagonal crystals with a center-to-center distance of 16 nm. A combination of quick-freeze/deep-etch images and our previous negative staining data indicate that the head domain of the uroplakin particle, which is exposed without an extensive glycocalyx shield, interacts closely with the head domains of the neighboring particles, while the membrane-embedded tail domains are farther apart; and that urothelial particles and plaques are not rigid structures as they can change their configuration in response to mechanical perturbations. Based on these data, we have constructed three-dimensional models depicting the structural organization of urothelial particles and plaques. Our models suggest that the head-to-head interaction may play a key role in determining the shape and size of the urothelial plaques. These models can explain many properties of urothelial plaques including their unique shape, detergent-insolubility, and morphological changes during vesicle maturation.

Animals↗
PubMed1996

Thermodynamics of the unfolding and spectroscopic properties of the V66W mutant of Staphylococcal nuclease and its 1-136 fragment.

Spectroscopic studies have been performed to characterize the solution structure of the V66W mutant of Staphylococcal nuclease and the corresponding 1-136 fragment, referred to as V66W'. Whereas wild-type nuclease has a single tryptophan residue at position 140, the V66W mutant has a second tryptophan residue at position 66, which is the only such residue in V66W'. Steady-state and time-resolved fluorescence studies show Trp-66 in V66W' to have a blue emission, a relatively large fluorescence quantum yield, a long lifetime, a significant degree of protection from solute quenchers, and to depolarize with a relatively long rotational correlation time. These results characterize Trp-66 in V66W' as being a buried residue, which indicates that this fragment retains some global structure. Circular dichroism (CD) data are consistent with the fragment having lost most of the alpha-helical content of the wild type, while retaining beta-sheet structure. The CD spectrum in the aromatic region also suggests that Trp-66 in the fragment experiences an asymmetric environment, which is not identical to that in the full length mutant, V66W. In addition, optical detection of triplet state magnetic resonance (ODMR) spectroscopy can clearly resolve the tryptophan residues and demonstrates differences between the local environment of Trp-66 in V66W and in V66W', as well as small differences in the Trp-140 environment in wild type and in V66W. Guanidine-HCl induced and thermally induced unfolding studies were performed by simultaneously acquiring CD and fluorescence data as a function of the perturbation and then performing a global analysis of such multiple data sets in terms of two-state and three-state unfolding models. Whereas data for wild-type nuclease and the V66W' fragment are well characterized by a two-state unfolding model, data for the V66W mutant are better characterized by a three-state process. That is, both the denaturant- and temperature-induced unfolding of V66W involves the significant population of an equilibrium unfolding intermediate. Our global analyses yield thermodynamic parameters for the unfolding transitions, and we show that the data for V66W can be described by a constrained three-state model in which the transition of the intermediate to the fully unfolded state is fixed to have the same thermodynamic parameters that describe the unfolding of the V66W' fragment.

Calorimetry↗
PubMed2003

Annular remodeling in chronic ischemic mitral regurgitation: ring selection implications.

BACKGROUND: More precise understanding of annular remodeling in the evolution of chronic ischemic mitral regurgitation is needed to provide a more rational basis for optimal annuloplasty ring sizing and selection as well as the design of new reparative techniques. Three-dimensional in vivo data describing these geometric perturbations however are lacking. Using an ovine model of chronic myocardial infarction we determined the three-dimensional distortions of the mitral annulus associated with the development of chronic ischemic mitral regurgitation. METHODS: Ten sheep underwent placement of radiopaque markers on the left ventricle and mitral annulus as well as placement of snares around the second and third obtuse marginal coronary arteries. After 8 days biplane cinefluoroscopy provided three-dimensional marker data and snare occlusion created an inferior infarction. After 7 more weeks the animals were studied again. RESULTS: Severity of mitral regurgitation increased (0.6 +/- 0.5 to 2.5 +/- 0.7). Septal-lateral (2.99 +/- 0.20 cm to 3.64 +/- 0.35 cm, maximum dimension) and commissure-commissure (3.71 +/- 0.32 cm to 4.40 +/- 0.30 cm) mitral annular diameters and the lengths of the muscular (7.77 +/- 0.39 cm to 9.51 +/- 0.72 cm) and fibrous annular perimeters (3.36 +/- 0.37 cm to 3.85 +/- 0.39 cm, p < 0.0001 for all) increased while the height of the annular "saddle horn" above a best-fit plane fell (0.73 +/- 0.52 cm to 0.57 +/- 0.42 cm, minimum dimension, p = 0.01). CONCLUSIONS: These three-dimensional in vivo data reflect annular remodeling in chronic ischemic mitral regurgitation and suggest that mitral repair in this context should be aimed at preventing further lengthening of the intertrigonal distance, reducing the septal-lateral annular diameter to reestablish adequate leaflet coaptation, and restoring the saddle shape of the annulus.

Animals↗
PubMed1989

Effects of host hormonal status on binding of activated estrogen receptor to nuclei from R3230AC and 7,12-dimethylbenz[a]anthracene-induced mammary tumors.

The effects of various hormonal perturbations that alter growth of two different rat mammary tumors in vivo were investigated by study of the interactions of [3H]estradiol-charged estrogen receptors ([3H]ER) with tumor nuclei in vitro. Nuclei from the transplantable R3230AC adenocarcinoma were isolated after ovariectomy, estrogen treatment, or progesterone treatment. Saturable specific binding of [3H]ER to nuclei was assayed in this in vivo-like system. Scatchard analysis of [3H]ER-nuclear binding data indicated that these perturbations did not affect affinity, which ranged from Kd 1.0 to 2.4 nM. However, the number of [3H]ER-binding sites/nucleus was altered according to the treatment: intact rats, 94,500 +/- 4,200; ovariectomy, 70,400 +/- 3,200; ovariectomy plus estradiol, 82,100 +/- 5,800; and ovariectomy plus progesterone, 73,900 +/- 2,500. Nuclei from primary tumors induced by 7,12-dimethylbenz(a)anthracene displayed similar affinities for [3H]ER, although these tumors had fewer binding sites per nucleus. Animals bearing 7,12-dimethylbenz(a)-anthracene-induced tumors were either ovariectomized or made diabetic by administration of streptozotocin, perturbations that cause regression of the majority of tumors. The number of [3H]ER binding sites per nucleus, in tumors classified according to growth characteristics in host animals subsequent to hormonal perturbation, was: intact growing 36,300 +/- 3,400; ovex regressing, 15,400 +/- 3,400; ovex, estrogen-treated growing, 28,100 +/- 2,700; diabetic regressing, 19,500 +/- 2,400; diabetic static, 32,100 and diabetic growing, 42,000 +/- 7,100. These results indicate that (a) the number of nuclear ER-binding sites can be reduced by hormonal interventions that cause tumor regression and (b) endogenous ovarian hormones may play a role in regulating nuclear ER binding.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed2005

Perturbation of local endogenous expression by insertion of Pol I expression constructs into the genome of Trypanosoma brucei.

Manipulation of gene expression is a common tool for the elucidation of biological function. Here we investigated the effects of over-expression in trypanosomes of a small GTPase, TbRABX1, using 2D gel electrophoresis and mass-spectrometry. An over-expression construct was targeting to the tubulin locus of chromosome I for stable integration and expression. Unexpectedly we observed alterations to the expression of gene products, i.e., tubulin, from surrounding regions of the genome; this effect was shown to be general and not dependent on the identity of the ectopic gene being expressed. These data suggest that local perturbation of the genome by insertion of DNA constructs can have wider impacts on gene expression, which need to be monitored.

Animals↗
PubMed2005

Local influence in comparative calibration models under elliptical t-distributions.

In this paper we consider applications of local influence (Cook, 1986) to evaluate small perturbations in the model or data set in the context of structural comparative calibration (Bolfarine and Galea, 1995) assuming that the measurements obtained follow a multivariate elliptical distribution. Different perturbation schemes are investigated and an application is considered to a real data set, using the elliptical t-distribution.

Analysis of Variance↗
PubMed1993

Recovery potential of hepatocytes from inhibition of albumin secretion by cadmium.

The aim of this study was to examine albumin production, a typical liver-specific function, in hepatocytes treated with Cd and to examine the reversibility of the perturbations induced by the toxic metal. Cultures of freshly isolated rat hepatocytes were exposed to increasing amounts of Cd in modified Leibowitz L-15 medium for 20 h; the cells were then allowed to recover by further incubation in Cd-free medium for an additional period of 20 h. The levels of albumin secreted into the extracellular medium were determined by enzyme-linked immunosorbent assay and were found to be reduced by Cd in a concentration-dependent fashion over the first 20 h. Inhibition was seen at Cd concentrations that did not cause any loss of cellular viability (up to 0.5 microM Cd), as judged from the release of lactate dehydrogenase by the cells. After replacement of the exposure medium by Cd-free medium, the same pattern of diminished albumin secretion was obtained, revealing the persistence of the cytotoxic effects when recovery conditions were applied. Moreover, hepatocytes exposed to 0.5 microM Cd for 20 h and processed for visualization of albumin immunoreactive sites using protein A-gold and electron microscopy exhibited very low albumin-specific labeling as compared to the controls (0.6 +/- 0.05 vs. 20.0 +/- 2.6 gold particles/micron2). Intracellular glutathione levels were not significantly changed by Cd either after the initial exposure or after the incubation that followed in control medium. The accumulation of Cd by the cells, as measured by graphite furnace atomic absorption spectrophotometry, was concentration dependent. It remained stable after medium change, indicating that Cd efflux was negligible upon reestablishment of normal conditions. The present data show that the perturbations in albumin metabolism caused by Cd are not readily alleviated after the cells are returned to Cd-free medium, suggesting a limited short-term recovery potential against cytotoxic damage. The data also demonstrate that hepatocyte-specific functions can be used as sensitive indicators for the detection of cellular disturbances by hepatotoxins.

Albumins↗
PubMed2004

Linear fuzzy gene network models obtained from microarray data by exhaustive search.

BACKGROUND: Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are needed to interpret the resulting large and complex data sets. Rationally designed perturbations (e.g., gene knock-outs) can be used to iteratively refine hypothetical models, suggesting an approach for high-throughput biological system analysis. We introduce an approach to gene network modeling based on a scalable linear variant of fuzzy logic: a framework with greater resolution than Boolean logic models, but which, while still semi-quantitative, does not require the precise parameter measurement needed for chemical kinetics-based modeling. RESULTS: We demonstrated our approach with exhaustive search for fuzzy gene interaction models that best fit transcription measurements by microarray of twelve selected genes regulating the yeast cell cycle. Applying an efficient, universally applicable data normalization and fuzzification scheme, the search converged to a small number of models that individually predict experimental data within an error tolerance. Because only gene transcription levels are used to develop the models, they include both direct and indirect regulation of genes. CONCLUSION: Biological relationships in the best-fitting fuzzy gene network models successfully recover direct and indirect interactions predicted from previous knowledge to result in transcriptional correlation. Fuzzy models fit on one yeast cell cycle data set robustly predict another experimental data set for the same system. Linear fuzzy gene networks and exhaustive rule search are the first steps towards a framework for an integrated modeling and experiment approach to high-throughput "reverse engineering" of complex biological systems.

Artificial Intelligence↗