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PubMed2001

Delayed gastrocnemius muscle response to sudden perturbation in rehabilitated patients with anterior cruciate ligament reconstruction.

This nonrandomized, posttest-only comparison between two experimental groups and a control group compared the lower extremity muscle activation latencies of patients following rehabilitated unilateral anterior cruciate ligament (ACL) reconstruction (allograft or autograft bone-patellar tendon-bone tissue) and normal control subjects. Twenty-three subjects (seven allograft, eight autograft, eight normal control) of similar age, height, weight, isokinetic knee extensor, and flexor peak torque/bodyweight, functional capability (single leg broad jump and single leg vertical jump) and recreational activity level participated in this study. Experimental group subjects were 21.3+/-5 months (allograft) and 27.6+/-10 months (autograft) after surgery. Kinematic and electromyographic data were sampled during ten randomly timed unilateral perturbations. Experimental group gastrocnemius latencies were delayed (allograft 59.5+/-25 ms, autograft 69+/-20 ms) compared to the control group (31.8+/-11 ms). The allograft (r=0.80) and autograft (r=0.40) unilateral ACL reconstruction groups displayed moderate and weak positive relationships between anterior knee laxity and knee angular displacements following perturbation, respectively. Control group subjects did not display significant relationships between these variables (r=-0.07). In the allograft group there was also a moderate inverse relationship between gastrocnemius latency and knee angular displacement following perturbation (r=-72). The autograft (r=-0.06) and control (r=-0.21) groups did not show similar relationships between these variables. Delayed gastrocnemius latencies for the experimental groups suggested prolonged neuromuscular deficits during weight-bearing dynamic knee stabilization. Knee angular displacement magnitude following sudden perturbation was related more strongly to knee laxity and gastrocnemius latency among subjects who had undergone ACL reconstruction using allograft bone-patellar tendon-bone tissue.

Adult↗
PubMed2005

Measuring the geometry of the universe in the presence of isocurvature modes.

The cosmic microwave background (CMB) anisotropy constrains the geometry of the Universe because the positions of the acoustic peaks of the angular power spectrum depend strongly on the curvature of three-dimensional space. In this Letter we exploit current observations to determine the geometry in the presence of isocurvature modes. Most previous analyses assumed that the primordial perturbations were adiabatic. A priori one might expect that allowing isocurvature modes would substantially degrade constraints on the curvature. We find, however, that with additional data sets, the geometry remains well constrained. When the most general isocurvature perturbation is allowed, the CMB alone can only poorly constrain the geometry to . Including large-scale structure data, one obtains Ohm(0) = 1.07 +/- 0.03, and 1.06 +/- 0.02 when supplemented by supernova data and the determination of H(0).

Journal Article↗
PubMed2005

A coherent framework for multiresolution analysis of biological networks with "memory": Ras pathway, cell cycle, and immune system.

Various biological processes exhibit characteristics that vary dramatically in response to different input conditions or changes in the history of the process itself. One of the examples studied here, the Ras-PKC-mitogen-activated protein kinase (MAPK) bistable pathway, follows two distinct dynamics (modes) depending on duration and strength of EGF stimulus. Similar examples are found in the behavior of the cell cycle and the immune system. A classification methodology, based on time-frequency analysis, was developed and tested on these systems to understand global behavior of biological processes. Contrary to most traditionally used statistical and spectral methods, our approach captures complex functional relations between parts of the systems in a simple way. The resulting algorithms are capable of analyzing and classifying sets of time-series data obtained from in vivo or in vitro experiments, or in silico simulation of biological processes. The method was found to be considerably stable under stochastic noise perturbation and, therefore, suitable for the analysis of real experimental data.

Algorithms↗
PubMed1976

Effects of angiotensin and prostaglandin A2 in perfused isolated kidneys of dogs.

Simultaneous recordings of pressure and flow were made from the renal artery in perfused isolate canine kidneys. The system was perturbated by the administration of angiotensin and prostaglandin A2. The data were recorded on frequency-modulated analog tape and converted to digital form, and a Fast Fourier Transform program was used to calculate input impedance. Changes in total renal volume and renal arterial pressure data were used to determine compliance values. in compliance were found, along with changes in both magnitude of impedance and phase angle, as a result of the perturbations introduced. Seemingly, renal vascular compliance has an important role in the autoregulatory mechanisms of the kidney.

Angiotensin II↗
PubMed1999

Mechanism of CheA protein kinase activation in receptor signaling complexes.

The chemotaxis receptor for aspartate, Tar, generates responses by regulating the activity of an associated histidine kinase, CheA. Tar is composed of an extracellular sensory domain connected by a transmembrane sequence to a cytoplasmic signaling domain. The cytoplasmic domain fused to a leucine zipper dimerization domain forms soluble active ternary complexes with CheA and an adapter protein, CheW. The kinetics of kinase activity within these complexes compared to CheA alone indicate approximately a 50% decrease in the KM for ATP and a 100-fold increase in the Vmax. A truncated CheA construct that lacks the phosphoaccepting H-domain and the CheY/CheB-binding domain forms an activated ternary complex that is similar to the one formed by the full-length CheA protein. The Vmax of H-domain phosphorylation by this complex is enhanced approximately 60-fold, the KM for ATP decreased to 50%, and the KM for H-domain decreased to 20% of the values obtained with the same CheA construct in the absence of receptor and CheW. The kinetic data support a mechanism of CheA regulation that involves perturbation of an equilibrium between an inactive form where the H-domain is loosely bound and an active form where the H-domain is tightly associated with the CheA active site and properly positioned for phosphotransfer. The data are consistent with an asymmetric mechanism of CheA activation [Levit, M., Liu, I., Surette, M. G., and Stock, J. B. (1996) J. Biol. Chem. 271, 32057-32063] wherein only one phosphoaccepting domain of CheA at a time can interact with an active center within a CheA dimer.

Bacterial Proteins↗
PubMed1997

Direct effect of type 1 human immunodeficiency virus (HIV-1) on intestinal epithelial cell differentiation: relationship to HIV-1 enteropathy.

Human immunodeficiency virus (HIV)-infected patients display severe impairments of gastrointestinal functions, including diarrhea and malabsorption, even in the absence of opportunistic infections. Since HIV-1 proteins and nucleic acids have been detected in several cell types of the intestinal mucosa, it has been postulated that HIV-1 itself could alter enterocytic functions. In the present study, we analyzed the effect of HIV-1 on the differentiation process of the epithelial intestinal cell clone HT-29-D4, which mimics the maturation of enterocytes along the crypt-villus axis of the small intestine. We found that HIV-1 infection impairs cellular differentiation (i) by affecting the barrier function of the epithelium, as evidenced by a decrease in the transepithelial electrical resistance, and (ii) by inhibiting the activity of one major glucose absorption function, i.e., sodium/glucose cotransport. At the morphological level, HIV-1 infection of HT-29-D4 cells was associated with the formation of lumina, which are representative of a defect in cellular organization. These morphofunctional perturbations induced by HIV-1 could be mimicked by nocodazole, a microtubule-disrupting agent. Correspondingly, HIV-1 exposure of HT-29-D4 cells evoked a massive disruption of microtubules, as revealed by alpha-tubulin indirect immunofluorescence staining. A similar effect was observed after incubation of the cells with either recombinant gp120 or a monoclonal antibody against galactosylceramide (GalCer), the intestinal receptor for HIV-1 gp120, suggesting that the effect of HIV-1 was mediated by the binding of gp120 to GalCer. Based on these data, we propose that HIV-1 may selectively alter enterocytic functions through a direct effect on the intracellular architecture of the cells. In contrast with previous theories for HIV-1 enteropathy, our data support the concept that HIV-1 may perturb intestinal functions without necessarily infecting intestinal epithelial cells.

Cell Differentiation↗
PubMed2005

Dynamics of nanoscopic water: vibrational echo and infrared pump-probe studies of reverse micelles.

The dynamics of water in nanoscopic pools 1.7-4.0 nm in diameter in AOT reverse micelles were studied with ultrafast infrared spectrally resolved stimulated vibrational echo and pump-probe spectroscopies. The experiments were conducted on the OD hydroxyl stretch of low-concentration HOD in the H2O, providing a direct examination of the hydrogen-bond network dynamics. Pump-probe experiments show that the vibrational lifetime of the OD stretch mode increases as the size of the reverse micelle decreases. These experiments are also sensitive to hydrogen-bond dissociation and reformation dynamics, which are observed to change with reverse micelle size. Spectrally resolved vibrational echo data were obtained at several frequencies. The vibrational echo data are compared to data taken on bulk water and on a 6 M NaCl solution, which is used to examine the role of ionic strength on the water dynamics in reverse micelles. Two types of vibrational echo measurements are presented: the vibrational echo decays and the vibrational echo peak shifts. As the water nanopool size decreases, the vibrational echo decays become slower. Even the largest nanopool (4 nm, approximately 1000 water molecules) has dynamics that are substantially slower than bulk water. It is demonstrated that the slow dynamics in the reverse micelle water nanopools are a result of confinement rather than ionic strength. The data are fit using time-dependent diagrammatic perturbation theory to obtain the frequency-frequency correlation function (FFCF) for each reverse micelle. The results are compared to the FFCF of water and show that the largest differences are in the slowest time scale dynamics. In bulk water, the slowest time scale dynamics are caused by hydrogen-bond network equilibration, i.e., the making and breaking of hydrogen bonds. For the smallest nanopools, the longest time scale component of the water dynamics is approximately 10 times longer than the dynamics in bulk water. The vibrational echo data for the smallest reverse micelle displays a dependence on the detection wavelength, which may indicate that multiple ensembles of water molecules are being observed.

Deuterium↗
PubMed2005

The effect of model approximations on single-collision distributions of low-energy electrons in liquid water.

The development of cross sections for the inelastic interaction of low-energy electrons with condensed tissue-like media is best accomplished within the framework of the dielectric theory. In this work we investigate the degree to which various model approximations, used in the above methodology, influence electron single-collision distributions. These distributions are of major importance to Monte Carlo track structure codes, namely, the energy-loss spectrum, the inelastic inverse mean free path, and the ionization efficiency. In particular, we make quantitative assessment of the influence of (1) the optical data set, (2) the dispersion algorithm, and (3) the perturbation and exchange Born corrections. It is shown that, although the shape and position of the energy-loss spectrum remains almost fixed, its peak height may vary by up to a factor of 1.5. Discrepancies in the calculated inelastic inverse mean free path are largely within 20-30% above 100 eV; they increase drastically, though, at lower energies. Exchange and perturbation Born corrections increase gradually below 1 keV leading to a approximately 30 to 40% reduction of the inverse mean free path at 100 eV. The perturbation effect contributes more than the exchange effect to this reduction. Similar to the dispersion situation, the effect of Born corrections at lower energies is also unclear since the models examined disagree strongly below 100 eV. In comparison, the vapor data are higher than the liquid calculations by 20 to 50% as the energy decreases from 1 to 0.1 keV, respectively. The excitation contribution is the main cause of this difference, since the ionization efficiency in the liquid levels off at approximately 90%, whereas the plateau value for the vapor is approximately 70%. It is concluded that electron inelastic distributions for liquid water, although in some respects distinctively different from the vapor phase, have associated uncertainties that are comparable in magnitude to the phase differences. The situation below 100 eV is uncertain.

Computer Simulation↗
PubMedDate not supplied

Multivariate curve resolution methods in imaging spectroscopy: influence of extraction methods and instrumental perturbations.

Imaging spectroscopy is becoming a key field of analytical chemistry. In the face of more and more complex samples, we actually need accurate microscopic insight. Nowadays, the methods used to produce concentration maps of the pure compounds from spectral data sets are based on the classical univariate approach although multivariate approaches are sometimes investigated. But in any case, the analytical quality of the chemical images thus provided cannot be discussed since no reference methods are at our disposal. Thus the proposed research focuses on the application of multivariate methods such as Orthogonal Projection Approach (OPA), SIMPLE-to-use Self-modeling Mixture Analysis (SIMPLISMA), Multivariate Curve Resolution - Alterning Least Squares (MCR-ALS), and Positive Matrix Factorization (PMF) for imaging spectroscopy. A systematic and quantitative characterization of the accuracy of spectra and images extraction is investigated on mid-infrared spectral data sets. Of special interest is the influence of instrumental perturbations such as noise and spectral shift on the extraction ability to access the algorithm's robustness.

Journal Article↗
PubMed1984

Sequence-specific recognition of DNA. Nuclear magnetic resonance assignments and structural comparison of wild-type and mutant lambda OR3 operator DNA.

The resonances of all the base protons and most of the sugar protons in both strands of the 17 base-pair OR3 operator of the phage lambda, and of the vC3 single base-pair mutant, have been assigned using two-dimensional nuclear magnetic resonance methods. The chemical shift and nuclear Overhauser effect data for these two DNA sequences reveal no structural perturbation at sites distal to the mutation, neither are there significant changes in structure immediately surrounding the altered base-pair in the mutant sequence. These results are consistent with the model proposed by Ohlendorf et al. (1982), based on crystallographic data on the cro protein, for the OR3-cro protein interaction. The data from these solution studies are examined and discussed in the light of this model. This work demonstrates that nuclear magnetic resonance chemical shifts and nuclear Overhauser effect intensities provide a method for comparing the solution structures of DNA molecules. From the resolution available in the spectra of the 17 base-pair operators studied, it is clear that DNA duplexes of up to 30 or more base-pairs can be studied using phase-sensitive methods.

Bacteriophage lambda↗
PubMed1998

Suitability of minidisc (MD) recordings for voice perturbation analysis.

A new digital recording format, Minidisc (MD), shows promise for high-quality voice recordings. It is available in a portable size and uses magneto-optical recording techniques on a miniature compact disc. The disc can be recorded an unlimited number of times with essentially the same playback life span: however, the digital recording technique uses a data compression algorithm that may interfere with acoustic voice perturbation analysis. This study investigated what effects this compression may have and whether the MD format is viable for use in this application. The MD format was evaluated by traditional synthetic test signals used on recording devices. In addition, human phonation recorded on Digital Audio Tape (DAT) was used as the input to the MD. The output of the MD was then compared to the original DAT recording. The two signals were analyzed for long- and short-term perturbation measures, and their waveforms were visually inspected. The results indicated that the MD format performed as well as the DAT format in all areas of standard tests, with the exception of signal-to-noise (S/N) ratio. S/N ratio for the MD was approximately 10 dB less than for the DAT under normal operating conditions; however, in comparing perturbation measures on normal human vowels, there were no significant differences between the two formats, i.e., no distortions in voice perturbation were introduced by the MD record/playback process.

Female↗
PubMed2004

Energy-based modeling as a basis for the analysis of reproductive data with the midge (Chironomus riparius).

We propose a biologically based approach to analyze reproductive data for the midge (Chironomus riparius). We showed in a previous study that its larval development can be divided in two distinct phases regarding the use of energy: The somatic growth period and the gametic growth period. We hypothesize here the gametic period to be a crucial period for the energetic investment for reproduction. To test this, we performed several assays with different feeding programs. Our results confirmed that energetic investment for reproduction mainly occurs during the gametic growth period. We could then propose energy-based models to analyze reproductive data. We assumed the effects to result from a perturbation in the use of energy. Two models corresponding to different physiological modes of actions--decreased efficiency of feeding (i.e., feeding decrease model) or increased cost of egg production (i.e., egg-cost increase model)--were built and used for the analysis of data obtained after an exposure to an artificially copper-spiked sediment. During this experiment, different exposure patterns were performed to investigate whether effects on reproduction resulted mainly from an exposure that occurs during the gametic growth period or from an exposure that occurs during the somatic growth period. These exposure patterns led to similar effects on reproduction, which suggests that the toxicant-induced stress persists during the whole life cycle, even in case of exposure occurring only during part of it. Both the feeding decrease model and egg-cost increase model were able to describe the data. We showed that addition of copper in the sediment, even in low quantity (<6.5 mg/kg), might affect reproduction at the individual level. If no-effect concentrations were derived from these results, this may lead to an overprotective value. A relevant no-effect concentration could be derived from further investigations at the population level.

Animals↗
PubMed2005

Evi3, a zinc-finger protein related to EBFAZ, regulates EBF activity in B-cell leukemia.

Retroviral insertions that activate proto-oncogenes are a primary cause of tumors in certain strains of mice. The AKXD recombinant inbred mice are predisposed to a variety of leukemias and lymphomas as a result of viral integration. One common insertion site, the ecotropic viral insertion site 3 (Evi3), has been implicated in most B-cell tumors in the AKXD-27 strain. The Evi3 gene encodes a zinc-finger protein with sequence similarity to the Early B-cell Factor-Associated Zinc-finger gene (EBFAZ). We show that the Evi3 gene is overexpressed in several tumors with viral insertions at Evi3, which results in the upregulation of Early B-cell Factor (EBF)-target gene expression, suggesting that Evi3 modulates EBF activity. Reconstitution of primary leukemia cells showed that these tumors express high densities of the B-cell surface proteins CD19 and CD38, which are EBF targets. Using a transactivation assay, we show that the terminal six zinc-fingers of Evi3 are required for modification of EBF activity. This is the first evidence that Evi3 expression in tumors alters the level of EBF target genes, and the first characterization of the Evi3 protein domains required for modulation of EBF activity. Further, these data imply that Evi3 misexpression initiates tumorigenesis by perturbing B-cell development via an interaction with EBF.

ADP-ribosyl Cyclase↗
PubMed2001

The role of gicerin, a novel cell adhesion molecule, in development, regeneration and neoplasia.

Neurite outgrowth factor (NOF) is an extracellular matrix (ECM) protein in the laminin family and its ligand, gicerin, is a novel cell adhesion molecule in the immunoglobulin superfamily. Gicerin has a homophilic adhesive activity as well as a heterotypic manner to NOF. In the nervous systems, gicerin is expressed during developmental stage when neurons migrate or extend neurites to form a neural network. Gicerin promotes neurite extension and migration of embryonic neurons in vitro by its homophilic and heterophilic adhesion activities. Introduction of antigicerin antibody into early developing eyes perturbs the layer formation of neural retina. These data suggest that gicerin participates in the formation of neural tissues. Gicerin is also expressed in other non-neural tissues; in epithelia of trachea, kidney and oviduct, gicerin expression is restricted in the developmental period. In contrast, muscular tissues and endothelial cells express gicerin continuously even after maturation. Interestingly, gicerin re-appears strongly in the regenerating epithelia of trachea, kidney and oviduct, and also anti-gicerin antibody disrupts the healing process of trachea. Furthermore, gicerin and NOF are overexpressed in the chicken nephroblastomas (Wilm's tumor) and oviductal adenocarcinomas. In vitro analyses show that gicerin adhesive activities can promote binding among tumor cells and adhesion of tumor cells to NOF. A polyclonal antibody against gicerin also perturbs the re-attachment of cancer cells onto metastasizing sites. It is clear from these studies that gicerin is a potential effector for pathological tissue formation as well as for normal development.

Animals↗
PubMed2006

Transcriptional dysregulation in Down syndrome: predictions for altered protein complex stoichiometries and post-translational modifications, and consequences for learning/behavior genes ELK, CREB, and the estrogen and glucocorticoid receptors.

The phenotype of Down syndrome, trisomy of chromosome 21, is hypothesized to be produced by the increased expression due to gene dosage of normal chromosome 21 genes. Chromosome 21 encodes a number of proteins that, based on experimental evidence or domain composition, are classed as transcription factors or their co-regulators. Other chromosome 21 proteins contribute to post-translational modification of transcription factors, including their phosphorylation, dephosphorylation and sumoylation. Several of these chromosome 21 proteins and the pathways in which they function have overlapping transcription factor specificities. Thus, altered stoichiometry in complexes and altered levels of activation of individual transcription factors may contribute to the Down syndrome phenotype by perturbation of downstream gene expression. Here we review recent data on four chromosome 21 proteins: NRIP1, GABPA, DYRK1A and SUMO3. We discuss the implications for activation of ELK, CREB, C/EBP alpha, beta estrogen and glucocorticoid receptors, and for expression of BDNF. Each of these proteins is relevant to learning, behavior and/or development and therefore perturbation of their activation may contribute to the Down syndrome phenotype.

Chromosome Mapping↗
PubMedDate not supplied

C-peptide and central nervous system complications in diabetes.

Substantial evidence collected from clinical data and experimental studies has indicated that CNS is not spared from diabetes complications. Impairments in CNS function are well documented in both type 1 and type 2 diabetic patients as well as in various animal models of diabetes, in terms of alterations in cognition, neuropsychology, neurobehavior, electrophysiology, structure, neurochemistry and apoptotic activities. These data suggest that primary diabetic encephalopathy exists as a definable diabetic complication. The mechanisms underlying this CNS complication are not clear. Experimental studies have suggested that neuronal apoptosis may play an important role in neuronal loss and impaired cognitive function. In diabetes multiple factors are responsible for neuronal apoptosis, such as a perturbed IGF system, hyperglycemia and the aging process itself. Recent data suggest that insulin/C-peptide deficiency may exert an eminent role. Administration of C-peptide partially corrects the perturbed IGF system in the brain and prevents neuronal apoptosis in hippocampus of type 1 diabetes. In neuroblastoma SH-SY5Y cells C-peptide provides a dose-dependent stimulation on cell proliferation and an anti-apoptotic effect as well. These studies provide a basis for administration of C-peptide as a potentially effective therapy for type 1 diabetes.

Aging↗
PubMed2005

Cognitive control under contingencies in anxious and depressed adolescents: an antisaccade task.

BACKGROUND: Emotion-related perturbations in cognitive control characterize adult mood and anxiety disorders. Fewer data are available to confirm such deficits in youth. Studies of cognitive control and error processing can provide an ideal template to examine these perturbations. Antisaccade paradigms are particularly well suited for this endeavor because they provide exquisite behavioral measures of modulation of response errors. METHODS: A new monetary reward antisaccade task was used with 28 healthy, 11 anxious, and 12 depressed adolescents. Performance accuracy, saccade latency, and peak velocity of incorrect responses were analyzed. RESULTS: Performance accuracy across all groups was improved by incentives (obtain reward, avoid punishment). However, modulation of saccade errors by incentives differed by groups. In incentive trials relative to neutral trials, inhibitory efficiency (saccade latency) was enhanced in healthy, unaffected in depressed, and diminished in anxious adolescents. Modulation of errant actions (saccade peak velocity) was improved in the healthy group and unchanged in both the anxious and depressed groups. CONCLUSIONS: These findings provide grounds for testing hypotheses related to the impact of motivation deficits and emotional interference on directed action in adolescents with mood and anxiety disorders. Furthermore, neural mechanisms can now be examined by using this task paired with functional neuroimaging.

Adolescent↗
PubMed2005

Intrinsic musculoskeletal properties stabilize wiping movements in the spinalized frog.

The mechanical stability properties of hindlimb-hindlimb wiping movements of the spinalized frog were examined. One hindlimb, the wiping limb, was implanted with 12 electromyographic (EMG) electrodes and attached to a robot that both recorded its trajectory and applied brief force perturbations. Cutaneous electrical stimulation was applied to the other hindlimb, the target limb, to evoke the hindlimb-hindlimb wiping reflex. Kinematic and EMG data from both unperturbed trials and trials in which a phasic perturbation was applied were collected from each spinalized frog. In the perturbed behaviors, we found that the initially large displacement attributable to the perturbation was compensated such that the final position was statistically indistinguishable from the unperturbed final position in all of the frogs, thus indicating the dynamic stability of these movements. This stability was robust to the range of perturbation amplitudes and nominal kinematic variation observed in this study. In addition, we investigated the extent to which intrinsic viscoelastic properties of the limb and proprioceptive feedback play a role in stabilizing the movements. No significant changes were seen in the EMGs after the perturbation. Furthermore, deafferentation of the wiping limb did not significantly affect the stability of the wiping reflex. Thus, we found that the intrinsic viscoelastic properties of the hindlimb conferred robust stability properties to the hindlimb-hindlimb wiping behavior. This stability mechanism may simplify the control required by the frog spinal motor systems to produce successful movements in an unpredictable and varying environment.

Animals↗