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Responses of sagittally aligned Purkinje cells during perturbed locomotion: synchronous activation of climbing fiber inputs.

1. These experiments were performed to test the hypothesis that climbing fiber inputs to sagittally aligned Purkinje cells located in a single folium are activated synchronously in response to a perturbation of the step cycle that interrupts the trajectory of the ipsilateral forelimb. 2. The experiments were performed in acutely decerebrate ferrets capable of walking spontaneously on a moving treadmill. A multiple single-unit recording technique was employed utilizing a fixed array of five sagittally oriented electrodes with electrode tips approximately 200 microns apart. 3. The extent to which the climbing fiber inputs to the recorded Purkinje cells were activated synchronously by the perturbation was calculated for individual trials by determining the synchrony index, a measure of the fraction of the cells responding to each perturbation. 4. The data indicate that there was a statistically significant increase in the synchronous activation of climbing fiber inputs at times immediately after the perturbation. No comparable complex spike modulation was found at the same phase of the unperturbed step cycle. 5. The specific combinations of climbing fiber inputs to neighboring Purkinje cells activated by successive perturbations varied from trial to trial. 6. The implications of these observations are discussed in the context of the nature of the inputs encoded by climbing fiber activation and the role of this afferent system in cerebellar cortical information processing.

Animals↗

Alternative method for minimal model analysis of intravenous glucose tolerance data.

The minimal models of glucose-insulin kinetics were used to analyze sets of data obtained from human subjects and dogs during frequently sampled intravenous glucose tolerance tests (FSIGTs). Analysis of some data sets from both species resulted in poor identification of parameters. To improve the parameter resolution, the information base on which the parameters are estimated was enlarged. This was accomplished by incorporating into the analysis 1) glucose data obtained between 0 and 8 min of the FSIGT and some of the insulin data obtained prior to the insulin peak and 2) a second set of FSIGT data for each individual obtained during a physiological perturbation. As a result, data analysis was considerably enhanced, with parameter fractional standard deviation being routinely reduced to less than 0.5. Analysis of stimulated data with noise levels for glucose and insulin set between 0.05 and 0.15 confirmed the improvement in parameter estimates. This modified approach to analysis of FSIGTs therefore consistently leads to well-defined kinetic descriptions of experimental data in various situations and supports the usefulness of the minimal model in examining the complex interplay between the parameters that influence overall glucose tolerance.

Adult↗

Assessing influence in regression analysis with censored data.

In this paper we show how to evaluate the effect that perturbations to the model, data, or case weights have on maximum likelihood estimates from censored survival data. The ideas and methods also apply to other nonlinear estimation problems. We review the ideas behind using log-likelihood displacement and local influence methods. We describe new interpretations for some local influence statistics and show how these statistics extend and complement traditional case deletion influence statistics for linear least squares. These statistics identify individual and combinations of cases that have important influence on estimates of parameters and functions of these parameters. We illustrate the methods by reanalyzing the Stanford Heart Transplant data with a parametric regression model.

Age Factors↗

Soft core thermodynamics from self-consistent hard core fluids.

In an effort to generalize the self-consistent Ornstein-Zernike approximation (SCOZA)-an accurate liquid state theory that has been restricted so far to hard core systems-to arbitrary soft core systems we study a combination of SCOZA with a recently developed perturbation theory. The latter was constructed by Ben-Amotz and Stell [J. Phys. Chem. B 108, 6877 (2004)] as a reformulation of the Weeks-Chandler-Andersen [J. Chem. Phys. 54, 5237 (1971)] perturbation theory directly in terms of an arbitrary hard sphere reference system. We investigate the accuracy of the combined approach for the Lennard-Jones fluid in comparison with simulation data and pure perturbation theory predictions and determine the dependence of the thermodynamic properties and the phase behavior on the choice of the effective hard core diameter of the reference system.

Journal Article↗

Determination of in vivo oxygen uptake and carbon dioxide evolution rates from off-gas measurements under highly dynamic conditions.

In vivo kinetics of Saccharomyces cerevisiae are studied, in a time window of 150 s, by analyzing the response of O(2) and CO(2) in the fermentor off-gas after perturbation of chemostat cultures by metabolite pulses. Here, a new mathematical method is presented for the estimation of the in vivo oxygen uptake rate (OUR) and carbon dioxide evolution rate (CER) directly from the off-gas data in such perturbation experiments. The mathematical construction allows effective elimination of delay and distortion in the off-gas measurement signal under highly dynamic conditions. A black box model for the fermentor off-gas system is first obtained by system identification, followed by the construction of an optimal linear filter, based on the identified off-gas model. The method is applied to glucose and ethanol pulses performed on chemostat cultures of S. cerevisiae. The estimated OUR is shown to be consistent with the independent dissolved oxygen measurement. The estimated in vivo OUR and CER provide valuable insights into the complex dynamic behavior of yeast and are essential for the establishment and validation of in vivo kinetic models of primary metabolism.

Bioreactors↗

The accurate electron crystallographic refinement of organic structures containing heavy atoms.

Prospects for the accurate structure determination of heavy-atom-containing organic crystals were evaluated with electron diffraction data from perchloro and perbromo derivatives of copper phthalocyanine. While the extensive overlap of experimental Patterson maps (from 1200kV intensities) with respective crystal autocorrelation functions explains the success of previous direct structure analyses, it is clear that multiple-scattering perturbations still evident at high voltage will frustrate the determination of accurate bond distances and angles. If, however, the result obtained after direct structure analysis and Fourier refinement is used to position an idealized molecular model (i.e. with chemically reasonable bonding parameters), the correct structure can then be justified by a rotational search coupled with a multislice dynamical calculation. Even though dynamical scattering is not the only major perturbation to such data sets, the resolution-limited correction is still sufficient to identify the correct molecular orientation in the unit cell. Alternatively, an acceptable unconstrained structure refinement can be carried out via a procedure proposed by Huang, Liu, Gu, Xiong, Fan & Li [Acta Cryst. (1996), A52, 152-157]. A phenomenological adjustment of observed intensities, based initially on the heavy-atom positions found in a high-resolution electron micrograph, will permit all light atoms to be observed near their ideal positions in the ensuing Fourier refinement.

Crystallization↗

Anharmonic vibrational properties of explosives from temperature-dependent Raman.

Raman spectra from 50 to 3500 cm(-1) and 4-296 K are analyzed for molecular crystal powders of the explosives pentaerythritol tetranitrate (PETN), beta-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and the inert naphthalene. Temperature-dependent Raman spectroscopy is utilized for its sensitivity to anharmonic couplings between thermally populated phonons and higher frequency vibrations relevant to shock up-pumping. The data are analyzed with anharmonic perturbation theory, which is shown to have significant fundamental limitations in application to real data. Fitting to perturbation theory revealed no significant differences in averaged anharmonicities among the three explosives, all of which exhibited larger averaged anharmonicities than naphthalene by a factor of 3. Calculations estimating the multiphonon densities of states also failed to correlate clearly with shock sensitivity. However, striking differences in temperature-dependent lifetimes were obvious: PETN has long lived phonons and vibrons, HMX has long lived phonons but short lived vibrons, while TATB has short lived phonons and vibrons at low temperature. Naphthalene, widely used as a model system, has significantly different anharmonicities and density of states from any of the explosives. The data presented suggest the further hypothesis that hindered vibrational energy transfer in the molecular crystals is a significant factor in shock sensitivity.

Journal Article↗

Modeling genetic networks from clonal analysis.

In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine genes across the 99 colonies. The report is divided into two parts: the first part identifies significant pair-wise dependencies from the given binary matrix using linear correlation and mutual information. A new method is proposed to determine statistically significant dependencies estimated using the mutual information measure. In the second, a Bayesian approach is used to obtain an approximate description (equivalence class) of network structures. The robustness of linear correlation, mutual information and the equivalence class of networks is investigated with perturbation and decreasing colony number. Perturbation of the data was achieved by generating bootstrap realizations. The results are refined with biological knowledge. It was found that certain dependencies in the network are immune to perturbation and decreasing colony number and may represent robust features, inherent in the differentiation program of osteoblast progenitor cells. The methods to be discussed are generic in nature and not restricted to the experimental paradigm addressed in this study.

Animals↗

Randomized maps for assessing the reliability of patients clusters in DNA microarray data analyses.

OBJECTIVE: Clustering algorithms may be applied to the analysis of DNA microarray data to identify novel subgroups that may lead to new taxonomies of diseases defined at bio-molecular level. A major problem related to the identification of biologically meaningful clusters is the assessment of their reliability, since clustering algorithms may find clusters even if no structure is present. METHODOLOGY: Recently, methods based on random "perturbations" of the data, such as bootstrapping, noise injections techniques and random subspace methods have been applied to the problem of cluster validity estimation. In this framework, we propose stability measures that exploits the high dimensionality of DNA microarray data and the redundancy of information stored in microarray chips. To this end we randomly project the original gene expression data into lower dimensional subspaces, approximately preserving the distance between the examples according to the Johnson-Lindenstrauss (JL) theory. The stability of the clusters discovered in the original high dimensional space is estimated by comparing them with the clusters discovered in randomly projected lower dimensional subspaces. The proposed cluster-stability measures may be applied to validate and to quantitatively assess the reliability of the clusters obtained by a large class of clustering algorithms. RESULTS AND CONCLUSION: We tested the effectiveness of our approach with high dimensional synthetic data, whose distribution is a priori known, showing that the stability measures based on randomized maps correctly predict the number of clusters and the reliability of each individual cluster. Then we showed how to apply the proposed measures to the analysis of DNA microarray data, whose underlying distribution is unknown. We evaluated the validity of clusters discovered by hierarchical clustering algorithms in diffuse large B-cell lymphoma (DLBCL) and malignant melanoma patients, showing that the proposed reliability measures can support bio-medical researchers in the identification of stable clusters of patients and in the discovery of new subtypes of diseases characterized at bio-molecular level.

Algorithms↗

Direct induction of DNA hypermethylation in sea urchin embryos by microinjection of 5-methyl dCTP stimulates early histone gene expression and leads to developmental arrest.

The role of DNA methylation in gene inactivation has been studied extensively in vertebrates but it is not clear whether it serves similar functions in other organisms. We devised a novel approach to induce hypermethylation of both endogenous and injected DNA in the sea urchin Lytechinus pictus in order to study the effect of DNA methylation on gene expression in this invertebrate. By injecting 5-methyl dCTP either alone or together with a cloned DNA construct into fertilized sea urchin eggs, replicating DNA became hypermethylated from the random incorporation of the methylated nucleotide in place of cytosine during DNA synthesis. During subsequent rounds of replication, the injected 5-methyl dCTP became depleted but methylation at CpG sites was still elevated presumably due to the action of a methyltransferase enzyme. Using this approach, we studied the effect of hypermethylation on two members of the sea urchin multigene family, the early H2B and the late H2B genes. De novo methylation was shown to occur at known cis-regulatory regions of the genes. The effect of methylation on gene activity was probed using RNase protection assay. Methylation resulted in increased early H2B histone gene expression but had no effect on late H2B histone gene expression. These results demonstrate that methylation does not necessarily inactivate genes in the sea urchins as previously thought. Interestingly, the development of embryos injected with 5-methyl dCTP typically was arrested at the blastula stage, and analysis of the genomic DNA extracted from injected embryos showed a significant increase in the endogenous methylation content. These data suggest that perturbation of methylation patterns in developmental sea urchin embryos may be responsible for the developmental arrest through altering the gene expression pattern.

Animals↗

A syndrome of altered cardiovascular, craniofacial, neurocognitive and skeletal development caused by mutations in TGFBR1 or TGFBR2.

We report heterozygous mutations in the genes encoding either type I or type II transforming growth factor beta receptor in ten families with a newly described human phenotype that includes widespread perturbations in cardiovascular, craniofacial, neurocognitive and skeletal development. Despite evidence that receptors derived from selected mutated alleles cannot support TGFbeta signal propagation, cells derived from individuals heterozygous with respect to these mutations did not show altered kinetics of the acute phase response to administered ligand. Furthermore, tissues derived from affected individuals showed increased expression of both collagen and connective tissue growth factor, as well as nuclear enrichment of phosphorylated Smad2, indicative of increased TGFbeta signaling. These data definitively implicate perturbation of TGFbeta signaling in many common human phenotypes, including craniosynostosis, cleft palate, arterial aneurysms, congenital heart disease and mental retardation, and suggest that comprehensive mechanistic insight will require consideration of both primary and compensatory events.

Activin Receptors, Type I↗

Impacts of biodiversity loss on ocean ecosystem services.

Human-dominated marine ecosystems are experiencing accelerating loss of populations and species, with largely unknown consequences. We analyzed local experiments, long-term regional time series, and global fisheries data to test how biodiversity loss affects marine ecosystem services across temporal and spatial scales. Overall, rates of resource collapse increased and recovery potential, stability, and water quality decreased exponentially with declining diversity. Restoration of biodiversity, in contrast, increased productivity fourfold and decreased variability by 21%, on average. We conclude that marine biodiversity loss is increasingly impairing the ocean's capacity to provide food, maintain water quality, and recover from perturbations. Yet available data suggest that at this point, these trends are still reversible.

Animals↗

Polarization measurements in high-energy deuteron photodisintegration.

We present measurements of the recoil proton polarization for the d(gamma-->,p-->)n reaction at straight theta(c.m.) = 90 degrees for photon energies up to 2.4 GeV. These are the first data in this reaction for polarization transfer with circularly polarized photons. The induced polarization p(y) vanishes above 1 GeV, contrary to meson-baryon model expectations, in which resonances lead to large polarizations. However, the polarization transfer Cx does not vanish above 1 GeV, inconsistent with hadron helicity conservation. Thus, we show that the scaling behavior observed in the d(gamma,p)n cross sections is not a result of perturbative QCD. These data should provide important tests of new nonperturbative calculations in the intermediate energy regime.

Journal Article↗

Dual-modality imaging of function and physiology.

Dual-modality imaging is a technique in which computed tomography (CT) or magnetic resonance imaging is combined with positron emission tomography or single-photon emission CT to acquire structural and functional images with an integated system. The data are acquired in a single procedure; the patient remains on the scanner table while undergoing both x-ray and radionuclide studies to facilitate correlation between the structural and functional images. The resulting data can aid in localization, enabling more specific diagnosis than can be obtained with a conventional imaging study. In addition, the anatomic information can be used to compensate the correlated radionuclide data for physical perturbations such as photon attenuation, scatter radiation, and partial volume errors. Thus, dual-modality imaging provides a priori information that can improve both the visual quality and the quantitative accuracy of the radionuclide images. Dual-modality imaging systems are also being developed for biologic research involving small animals. Small-animal dual-modality systems offer advantages for measurements that currently are performed invasively with autoradiography and tissue sampling. By acquiring data noninvasively, dual-modality imaging permits serial studies in a single animal, enables measurements to be performed with fewer animals, and improves the statistical quality of the data.

Animals↗

Neuronal and glial calcium signaling in Alzheimer's disease.

Cognitive impairment and emotional disturbances in Alzheimer's disease (AD) result from the degeneration of synapses and death of neurons in the limbic system and associated regions of the cerebral cortex. An alteration in the proteolytic processing of the amyloid precursor protein (APP) results in increased production and accumulation of amyloid beta-peptide (Abeta) in the brain. Abeta has been shown to cause synaptic dysfunction and can render neurons vulnerable to excitotoxicity and apoptosis by a mechanism involving disruption of cellular calcium homeostasis. By inducing membrane lipid peroxidation and generation of the aldehyde 4-hydroxynonenal, Abeta impairs the function of membrane ion-motive ATPases and glucose and glutamate transporters, and can enhance calcium influx through voltage-dependent and ligand-gated calcium channels. Reduced levels of a secreted form of APP which normally regulates synaptic plasticity and cell survival may also promote disruption of synaptic calcium homeostasis in AD. Some cases of inherited AD are caused by mutations in presenilins 1 and 2 which perturb endoplasmic reticulum (ER) calcium homeostasis such that greater amounts of calcium are released upon stimulation, possibly as the result of alterations in IP(3) and ryanodine receptor channels, Ca(2+)-ATPases and the ER stress protein Herp. Abnormalities in calcium regulation in astrocytes, oligodendrocytes, and microglia have also been documented in studies of experimental models of AD, suggesting contributions of these alterations to neuronal dysfunction and cell death in AD. Collectively, the available data show that perturbed cellular calcium homeostasis plays a prominent role in the pathogenesis of AD, suggesting potential benefits of preventative and therapeutic strategies that stabilize cellular calcium homeostasis.

Adenosine Triphosphate↗

Luttinger-liquid behavior in weakly disordered quantum wires.

We have measured the temperature dependence of the conductance in long V-groove quantum wires fabricated in GaAs/AlGaAs heterostructures. Our data are consistent with recent theories developed within the framework of the Luttinger-liquid model, in the limit of weakly disordered wires. We show that, for the relatively low level of disorder in our quantum wires, the value of the interaction parameter g congruent with 0.66, which is the expected value for GaAs. However, samples with a higher level of disorder show conductance with stronger temperature dependence, which does not allow their treatment in the framework of perturbation theory. Fitting such data with perturbation-theory models leads inevitably to wrong (lower) values of g.

Journal Article↗

Prothrombotic and fibrinolytic function of normal and perturbed endothelium.

Endothelium mediates thrombosis and fibrinolysis in part through cell-based production and binding of coagulation factors and anticoagulant moieties. A variety of biologically active agents (homocysteine, interleukin-1, and endotoxin) and environmental factors (mechanical injury and hypoxia) can upset the homeostasis of the coagulation system leading in vitro and in vivo to abnormal propensity for thrombin formation. None of the above agents or any similar agents have been demonstrated to inhibit clotting factors or thrombosis formation. As one would expect, injury to endothelium even on a sublethal basis promotes a procoagulant response. This procoagulant response appears to be multifactorial and multiphasic. Gross injury leads to factor release by dead or dying cells with rapid promotion of thrombosis by neighboring infact cells. A more subtle prothrombotic state promulgated by viable cells appears after sublethal perturbation and is characterized by protein synthesis-dependent production of endothelial-produced clotting factors in the early stages of injury with subsequent return to normal levels of these factors by 24 hr. A second phase of abnormal levels of fibrinolysis inhibitors and possible reduction in fibrinolysis promoters appears to follow up to 48 hr after the initial injury. Thus the cell can be viewed as producing means of promoting thrombus formation followed by preventing thrombus dissolution. The data presented in this article are primarily cell culture data and are thus limited both in physiologic applicability and in ability to define over long periods the relevance of those findings to other cells in the hemostatic system. Nonetheless, in vivo data of endothelial perturbation correlate with the in vitro findings.(ABSTRACT TRUNCATED AT 250 WORDS)

Blood Coagulation↗

C-peptide prevents nociceptive sensory neuropathy in type 1 diabetes.

We examined the effects of C-peptide replacement on unmyelinated fiber function in the hind paw, sural nerve C-fiber morphometry, sciatic nerve neurotrophins, and the expression of neurotrophic receptors and content of neuropeptides in dorsal root ganglia in type 1 diabetic BB/Wor-rats. C-peptide replacement from onset of diabetes had no effect on hyperglycemia, but it significantly prevented progressive thermal hyperalgesia and prevented C-fiber atrophy, degeneration, and loss. These findings were associated with preventive effects on impaired availability of nerve growth factor and neurotrophin 3 in the sciatic nerve and significant prevention of perturbed expression of insulin, insulin growth factor-1, nerve growth factor, and neurotrophin 3 receptors in dorsal root ganglion cells. These beneficial effects translated into prevention of the decreased content of dorsal root ganglia nociceptive peptides such as substance P and calcitonin gene-related peptide. From these findings we conclude that replacement of insulinomimetic C-peptide prevents abnormalities of neurotrophins, their receptors, and nociceptive neuropeptides in type 1 BB/Wor-rats, resulting in the prevention of C-fiber pathology and nociceptive sensory nerve dysfunction. The data indicate that perturbed insulin/C-peptide action plays an important pathogenetic role in nociceptive sensory neuropathy and that C-peptide replacement may be of benefit in treating painful diabetic neuropathy in insulin-deficient diabetic conditions.

Animals↗