Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Perturbation data”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources
PubMed1991

Whole blood and plasma amino acid uptakes by lactating bovine mammary glands.

The objective of the experiment was to determine the contribution of red blood cells to transport of individual amino acids to lactating bovine mammary glands. Blood samples were collected from coccygeal and subcutaneous abdominal veins of 21 lactating Holstein cows on d 35, 70, 105, and 126 of lactation. Samples were collected every 20 min for 12 h. Subsamples of whole blood and plasma were pooled by hour and day. Hourly plasma samples and daily whole blood and plasma samples were analyzed for amino acid concentration. Plasma glutamate concentration was stable throughout the 12-h collection period, indicating that sample collection did not perturb amino acid homeostasis. Therefore, data from pooled daily samples were used for subsequent comparisons. Whole blood arteriovenous differences of phosphoserine, aspartate, glutamate, hydroxyproline, phosphoethanolamine, serine, asparagine, glycine, glutamine, taurine, histidine, citrulline, threonine, alanine, beta-aminoisobutyrate, carnosine, arginine, proline, alpha-aminobutyrate, tyrosine, valine, methionine, cystine, isoleucine, leucine, phenylalanine, tryptophan, ornithine, and lysine differed significantly from plasma arteriovenous differences. Uptakes of individual amino acids from plasma were poorly correlated with uptake from whole blood. These data clearly indicate that uptake data derived from plasma do not adequately represent whole blood amino acid uptake.

Amino Acids↗
PubMed1987

Increased neutrophil elastase activity in cigarette smokers.

We compared plasma levels of the neutrophil elastase-derived fibrinopeptide A-alpha-1-21 in healthy cigarette smokers with those in nonsmokers. The mean A-alpha-1-21 concentration was fivefold higher (95% confidence interval [CI], 3.0 to 9.6) in ten cigarette smokers than in 20 healthy nonsmokers (2.0 nmol/L compared with 0.4 nmol/L; p less than 0.0001). To evaluate the acute effect of smoking on enzyme activity, a second group of ten smokers was studied. After refraining from smoking for 12 hours, each person smoked three cigarettes. The mean A-alpha-1-21 level in the second group of smokers was not different from that in the first group of smokers (1.8 nmol/L compared with 2.0 nmol/L) but was fivefold higher (95% CI, 2.6 to 8.7) than that in the nonsmokers (1.8 nmol/L compared with 0.4 nmol/L; p less than 0.0001). After smoking three cigarettes, subjects had a twofold elevation (95% CI, 1.6 to 3.5) in the mean A-alpha-1-21 concentration (from 1.8 nmol/L to 4.1 nmol/L; p = 0.002). Our data show that cigarette smoking perturbs the in-vivo elastase-antielastase balance and thus may produce lung disease through this mechanism.

Adult↗
PubMed1975

Dissociation of rat parotid gland.

Rat parotid gland was dissociated by sequential collagenase and hyaluronidase digestions, chelation with ethylenediaminetetraacetic acid, and mild shearing force to yield predominantly single cells. The isolated acinar cells retained their morphologic characteristics and their amylase activity. The functional integrity of the isolated cells was assessed by measuring their secretory response to isoproterenol, epinephrine, and carbamylcholine and by their ability to incorporate radioactively labeled leucine and thymidine. The discharge of amylase from the dissociated cells was not effected by isoproterenol or norepinephrine and the response to carbamylcholine was minimal. The data indicate a destruction or perturbation of hormone receptors during the dissociation procedure. The maintenance of the cells in culture for up to 18 hours failed to restore the responsiveness of the isolated parotid gland acinar cells to isoproterenol. The isolated cells incorporated 14C-leucine into proteins at a linear rate between 30 and 180 minutes. Chromatographic and electrophoretic profiles of newly synthesized proteins indicated that all major proteins synthesized in vivo were also synthesized by the isolated cells. The isolated cells incorporated tritiated thymidine into DNA. Furthermore, stimulation of DNA synthesis by isoproterenol in vivo was reflected by a higher rate of thymidine incorporation by the isolated cells as compared with controls. The dissociated parotid gland cells offer a convenient system for studying various cellular processes, particularly the synthesis of macromolecules with high specific activity. However, some functions, notably the response to beta- adrenergic agonists, are lost during the dissociation procedure.

Amylases↗
PubMed1991

Effects of calcium buffering on the synthesis of the 26-kDa heat-shock protein family.

We have reported on the effect of heat in C127 cells having various basal levels of the Ca(2+)-binding proteins calmodulin (CaM) or parvalbumin [Evans, Simonette, Rasmussen, Means, and Tomasovic, J. Cell. Physiol. 142, 615-627 (1990)]. These studies suggested that induction of the synthesis of 26-kDa heat-shock protein (hsp-26) depended on increased intracellular free Ca2+ [Ca2+]i and that induction was abrogated by increased Ca(2+)-binding capacity. To evaluate further the role of [Ca2+]i in mediating the response to hyperthermia and the potential for Ca(2+)-buffering to affect these processes, we loaded C127 parental cells with the Ca2+ chelators BAPTA or quin-2 (5 microM for 60 min) and then immediately heated the cells (30 min at 43 degrees C) and labeled them (3 h at 37 degrees C) with [3H]leucine. Measurements of [Ca2+]i with quin-2 and fura-2 showed that an increase in [Ca2+]i occurred with this heat dose, but that the quin-2 buffered that increase. Two-dimensional gels showed that cells loaded with BAPTA and quin-2 had a reduced rate of synthesis of the most basic (nonphosphorylated) hsp-26a isoform. The apparent synthesis of the more acidic isoforms (hsp-26b, hsp-26c) was less affected, but labeling studies with 32P showed this reflected continued accumulation of these phosphorylated isoforms, especially the most highly phosphorylated hsp-26c. Although it reduced hsp-26a synthesis, the temporary buffering of [Ca2+]i did not alter the subsequent expression of heat killing or the extent of thermotolerance significantly, possibly because phosphorylated hsp-26 was still generated. These data support the hypothesis that perturbations of [Ca2+]i directly modulate induction of hsp-26a synthesis.

Acclimatization↗
PubMed1989

Increased erythrocyte membrane arachidonate and platelet malondialdehyde (MDA) production in psoriasis: normalization after fish-oil.

Evidence exists of platelet activation and increased thromboxane B2 production in psoriasis. In 13 patients suffering from psoriasis, we determined the lipid composition of erythrocyte membrane, erythrocyte and platelet glutathione peroxidase activity (E-GSH-Px; Plt-GSH-Px), platelet MDA production and bleeding time. Compared with normal controls, psoriatics showed a significant increase in erythrocyte membrane arachidonic acid (AA) (p less than 0.001) and polyunsaturated fatty acids (PUFA) (p less than 0.001), platelet MDA production (p less than 0.01) and E- and Plt-GSH-Px activity (p less than 0.01; p less than 0.01). After 8 weeks of fish-oil supplementation (20 ml/day) we observed the following changes: a) marked amelioration of skin lesions; b) normalization of membrane lipid pattern and platelet MDA production; c) a further increase in E- and Plt-GSH-Px activity (p less than 0.01; p less than 0.01); d) significant prolongation of bleeding time (p less than 0.05). Our data demonstrate: 1) a generalized perturbation of membrane lipid pattern in psoriasis, characterized by an excess of AA; 2) an activation of AA metabolism in platelets suggested by increased MDA production and GSH-Px activity; 3) dietary fish-oil may normalize membrane lipid pattern and reduce platelet hyperactivity in psoriasis.

Adult↗
PubMed1981

Preferential reactivity of certain human and rabbit IgM and IgG rheumatoid factors with mildly reduced and amidomethylated IgG.

Two broadly defined populations were identified in affinity column-enriched rabbit and human rheumatoid factor (RF) preparations: one population reacted preferentially with mildly reduced and alkylated (MRA) homologous (with regard to species) IgG, and the other reacted preferentially with native, intact IgG. Each of these reactivities was identified by preferential association of RF with either intact or MRA IgG-Sepharose 4B conjugates and existed in both the IgM and IgG immunoglobulin classes. Use of soluble IgG inhibitor preparations in RF- dependent hemolytic and hemagglutination inhibition in RF-dependent hemolytic and hemagglutination inhibition assays showed that the preferred form of IgG inhibitor paralleled the preference of a particular RF preparation for a particular IgG affinity matrix. In addition, preferential reactivity was observed toward either intact or MRA Fc gamma inhibitors. On a molar basis RF reactivity with Fc gamma was significantly less than that observed in the presence of whole IgG. In contrast, neither IgG Fab nor F(ab')2 fragments were reactive with either of the 2 specificity populations of RF. The distribution of immunoglobulin class relative to specificity suggested that preferential reactivity with MRA IgG was usually associated with IgM RF, and reactivity with intact IgG was usually associated with IgG RF. These data suggest that in vivo perturbation of IgG structure may lead to an RF response identifiable by reactivity with an altered monomeric form of IgG.

Amides↗
PubMed1997

Involvement of calcium-dependent protein kinase C in arsenite-induced genotoxicity in Chinese hamster ovary cells.

Arsenic is the first metal to be identified as a human carcinogen. Arsenite, one inorganic form of arsenic, has been found to induce sister chromatid exchange, chromosome aberrations, and gene amplification in a variety of in vitro systems. In this study of arsenite-induced genotoxicity represented a micronuclei production in Chinese hamster ovary cells (CHO-K1), we found that the calcium channel blocker, verapamil, can potentiate arsenite-induced micronuclei. And after arsenite treatment, the elevation of intracellular calcium was observed. When extracellular calcium was depleted during arsenite treatment, the arsenite-induced micronuclei formation was significantly suppressed. These data indicated that a calcium ion plays an essential role in arsenite-induced genotoxicity. Further, it was found that the cotreatment of arsenite and a calcium ionophore, A23187, can increase the micronuclei induction. In contrast, pretreatment of the intracellular calcium chelator, quin 2, significantly inhibited micronuclei production of arsenite administration. In addition, we measured the activity of calcium- and phospholipid-dependent protein kinase C (PKC) and found that arsenite can activate PKC activity in a dose-dependent manner. Subsequently, some PKC activators and inhibitors were applied to investigate the involvement of PKC on arsenite-induced micronuclei formation. It was found that H7, a PKC inhibitor, can depress but TPA, a PKC activator, can enhance arsenite-induced micronuclei significantly. These data indicated that arsenite exposure perturbs intracellular calcium homeostasis and activates PKC activity. As a result, the activation of PKC activity may play an important role in arsenite-induced genotoxicity.

Adenosine Triphosphate↗
PubMed2002

Cricothyroid approximation to elevate vocal pitch in male-to-female transsexuals: results of surgery.

Functional changes in voice production, including pitch elevation, may help male-to-female transsexuals assume a new gender identity. To date, there has been a paucity of objective data on the effectiveness of pitch-raising methods. Acoustic data were gathered with regard to preoperative and postoperative changes in pitch, pitch range, and perturbation in 20 patients after cricothyroid approximation. Subjective data were gathered by means of a mailed questionnaire. The mean follow-up time was 22 months. The speaking fundamental frequency was raised by half an octave without any significant changes in perturbation. The lower and upper limits of pitch range both increased by an average of 4 semitones. There was some decline over time of the lower pitch range toward preoperative levels, but the upper pitch range remained elevated. The majority of the patients were satisfied with the results of surgery and felt their voices to be more feminine.

Adult↗
PubMed2002

Myoglobin and cytochrome b5: a nuclear magnetic resonance study of a highly dynamic protein complex.

The transient complex of bovine myoglobin and cytochrome b(5) has been investigated using a combination of NMR chemical shift mapping, (15)N relaxation data, and protein docking simulations. Chemical shift perturbations observed for cytochrome b(5) amide resonances upon complex formation with either metmyoglobin (Fe(III)) or carbon monoxide-bound myoglobin (Fe(II)) are more than 10-fold smaller than in other transient redox protein complexes. From (15)N relaxation experiments, an increase in the overall correlation time of cytochrome b(5) in the presence of myoglobin is observed, confirming that complex formation is occurring. The chemical shift perturbations of proton and nitrogen amide nuclei as well as heme protons of cytochrome b(5) titrate with increasing myoglobin concentrations, also demonstrating the formation of a weak complex with a K(a) in the inverse millimolar range. The perturbed residues map over a wide surface area of cytochrome b(5), with patches of residues located around the exposed heme 6-propionate as well as at the back of the protein. The nature of the affected residues is mostly negatively charged contrary to perturbed residues in other transient complexes, which are mainly hydrophobic or polar. Protein docking simulations using the NMR data as constraints show several docking geometries both close to and far away from the exposed heme propionates of myoglobin. Overall, the data support the emerging view that this complex consists of a dynamic ensemble of orientations in which each protein constantly diffuses over the surface of the other. The characteristic NMR features may serve as a structural tool for the identification of such dynamic complexes.

Animals↗
PubMed2001

Cosmic microwave background anisotropies with mixed isocurvature perturbations.

In the light of the recent high quality data of the cosmic microwave background anisotropies, several estimations of cosmological parameters have been published. We study to what extent these estimations depend on assumptions about the initial conditions of the cosmological perturbations, which are usually supposed to be adiabatic. We show that, for more generic initial conditions, not only the best fit values are very different but the allowed parameter range enlarges dramatically. This raises the question which cosmological information (matter content of the Universe vs physics of inflation) can be reliably extracted from these data.

Journal Article↗
PubMed2003

A global sensitivity analysis of performance of a medical diagnostic test when verification bias is present.

Current advances in technology provide less invasive or less expensive diagnostic tests for identifying disease status. When a diagnostic test is evaluated against an invasive or expensive gold standard test, one often finds that not all patients undergo the gold standard test. The sensitivity and specificity estimates based only on the patients with verified disease are often biased. This bias is called verification bias. Many authors have examined the consequences of verification bias and have proposed bias correction methods based on the assumption of independence between disease status and election for verification conditionally on the test result, or equivalently on the assumption that the disease status is missing at random using missing data terminology. This assumption may not be valid and one may need to consider adjustment for a possible non-ignorable verification bias resulting from the non-ignorable missing data mechanism. Such an adjustment involves ultimately uncheckable assumptions and requires sensitivity analysis. The sensitivity analysis is most often accomplished by perturbing parameters in the chosen model for the missing data mechanism, and it has a local flavour because perturbations are around the fitted model. In this paper we propose a global sensitivity analysis for assessing performance of a diagnostic test in the presence of verification bias. We derive a region of all sensitivity and specificity values consistent with the observed data and call this region a test ignorance region (TIR). The term 'ignorance' refers to the lack of knowledge due to the missing disease status for the not verified patients. The methodology is illustrated with two clinical examples.

Diagnostic Tests, Routine↗
PubMed2003

Redox-active tyrosine residues: role for the peptide bond in electron transfer.

Photosystem II (PSII) catalyzes the light-driven oxidation of water and reduction of plastoquinone. In PSII, redox-active tyrosine Z conducts electrons between the primary chlorophyll donor and the manganese cluster, which is the catalytic site. In this report, difference FT-IR spectroscopy is used to show that oxidation of redox-active tyrosine Z causes perturbations of the peptide bond. PSII data were acquired on control samples, as well as samples in which tyrosine was 2H4 (ring)-labeled. Comparison to model compound data, acquired both from tyrosinate and its 2H4 isotopomer, was performed. The PSII FT-IR spectrum exhibited vibrational bands that are assignable to imide and amide vibrational modes. In previous work, we have shown that oxidation of tyrosinate perturbs the terminal amino group of tyrosinate (Ayala, I.; Range, K.; York, D.; Barry, B. A. J. Am. Chem. Soc. 2002, 124, 5496-5505). Density functional calculations on tyrosinate supported the interpretation that the perturbation is due to spin delocalization onto the amino group. In tyrosine-containing dipeptides, perturbations of the peptide bond were observed. Therefore, the imide and amide perturbations observed here are attributed to spin delocalization into the peptide bond in PSII. Migration of the electron hole in PSII may be consistent with peptide bond involvement in tyrosyl radical-based electron-transfer reactions.

Amides↗
PubMed2004

Modeling the demand reduction input-output (I-O) inoperability due to terrorism of interconnected infrastructures.

Interdependency analysis in the context of this article is a process of assessing and managing risks inherent in a system of interconnected entities (e.g., infrastructures or industry sectors). Invoking the principles of input-output (I-O) and decomposition analysis, the article offers a framework for describing how terrorism-induced perturbations can propagate due to interconnectedness. Data published by the Bureau of Economic Analysis Division of the U.S. Department of Commerce is utilized to present applications to serve as test beds for the proposed framework. Specifically, a case study estimating the economic impact of airline demand perturbations to national-level U.S. sectors is made possible using I-O matrices. A ranking of the affected sectors according to their vulnerability to perturbations originating from a primary sector (e.g., air transportation) can serve as important input to risk management. For example, limited resources can be prioritized for the "top-n" sectors that are perceived to suffer the greatest economic losses due to terrorism. In addition, regional decomposition via location quotients enables the analysis of local-level terrorism events. The Regional I-O Multiplier System II (RIMS II) Division of the U.S. Department of Commerce is the agency responsible for releasing the regional multipliers for various geographical resolutions (economic areas, states, and counties). A regional-level case study demonstrates a process of estimating the economic impact of transportation-related scenarios on industry sectors within Economic Area 010 (the New York metropolitan region and vicinities).

Journal Article↗
PubMed2005

Tracking perturbations in Boolean networks with spectral methods.

In this paper we present a method for predicting the spread of perturbations in Boolean networks. The method is applicable to networks that have no regular topology. The prediction of perturbations can be performed easily by using a presented result which enables the efficient computation of the required iterative formulas. This result is based on abstract Fourier transform of the functions in the network. In this paper the method is applied to show the spread of perturbations in networks containing a distribution of functions found from biological data. The advances in the study of the spread of perturbations can directly be applied to enable ways of quantifying chaos in Boolean networks. Derrida plots over an arbitrary number of time steps can be computed and thus distributions of functions compared with each other with respect to the amount of order they create in random networks.

Journal Article↗
PubMed2000

Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose.

Parallel processing is more stable than serial processing in many areas that employ interconnected activities. This hypothesis was tested for microbial community function using two quadruplicate sets of methanogenic communities, each set having substantially different populations. The two communities were maintained at a mean cell residence time of 16 days and a mean glucose loading rate of 0.34 g/liter-day in variable-volume reactors. To test stability to perturbation, they were subjected to an instantaneous glucose pulse that resulted in a 6.8-g/liter reactor concentration. The pattern of accumulated products in response to the perturbation was analyzed for various measures of functional stability, including resistance, resilience, and reactivity for each product. A new stability parameter, "moment of amplification envelope," was used to compare the soluble compound stability. These parameters indicated that the communities with predominantly parallel substrate processing were functionally more stable in response to the perturbation than the communities with predominantly serial substrate processing. The data also indicated that there was good replication of function under perturbed conditions; the degrees of replication were 0.79 and 0.83 for the two test communities.

Bioreactors↗
PubMed2005

Unravelling the functional interaction structure of a cellular network from temporal slope information of experimental data.

Due to the unavoidable nonbiological variations accompanying many experiments, it is imperative to consider a way of unravelling the functional interaction structure of a cellular network (e.g. signalling cascades or gene networks) by using the qualitative information of time-series experimental data instead of computation through the measured absolute values. In this spirit, we propose a very simple but effective method of identifying the functional interaction structure of a cellular network based on temporal ascending or descending slope information from given time-series measurements. From this method, we can gain insight into the acceptable measurement error ranges in order to estimate the correct functional interaction structure and we can also find guidance for a new experimental design to complement the insufficient information of a given experimental dataset. We developed experimental sign equations, making use of the temporal slope sign information from time-series experimental data, without a specific assumption on parameter perturbations for each network node. Based on these equations, we further describe the available specific information from each part of experimental data in detail and show the functional interaction structure obtained by integrating such information. In this procedure, we use only simple algebra on sign changes without complicated computations on the measured absolute values of the experimental data. The result is, however, verified through rigorous mathematical definitions and proofs. The present method provides us with information about the acceptable measurement error ranges for correct estimation of the functional interaction structure and it further leads to a new experimental design to complement the given experimental data by informing us about additional specific sampling points to be chosen for further required information.

Cell Physiological Phenomena↗
PubMed1989

The cold-induced denaturation of lactate dehydrogenase at sub-zero temperatures in the absence of perturbants.

The cold-induced denaturation of lactate dehydrogenase has been determined in an unfrozen, cryoprotectant free solution at sub-zero temperatures. The cold-induced denaturation temperature (TL) has been found to be -28 degrees C. The results for the first time clearly establish that temperature alone can induce denaturation in a cooled protein solution. The validity of earlier data, obtained in the presence of perturbants (particularly pH or guanidinium chloride), is discussed.

Animals↗
PubMed2001

Cell cycle-dependent protein secretion by Saccharomyces cerevisiae.

Synchronized Saccharomyces cerevisiae cell populations were used to examine secretion rates of a heterologous protein as a function of cell cycle position. The synchronization procedure had a profound effect on the type and quality of data obtained. When cell synchrony was induced by cell cycle-arresting drugs, a significant physiological perturbation of cells was observed that obscured representative secretion data. In contrast, synchronization with centrifugal elutriation resulted in synchronized first-generation daughter cells with undetectable perturbation of the physiological state. The synchronized cells did not secrete significant amounts of protein until they reached cell division, suggesting that the secretion process in these cells is strongly cell cycle dependent. However, the maximum secretion rate of the synchronized culture (7-14 molecules/cell/second) was significantly lower than that of an asynchronous culture (29-51 molecules/cell/second). This result indicates that young daughter cells isolated in the synchronization process exhibit different protein secretion behavior than older mother cells that are absent in the synchronized cell population but present in the asynchronous culture.

Cell Cycle↗