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 145 records · Page 8Linked to original sources
PubMed2005

Role of apolipoproteins in gammadelta and NKT cell-mediated innate immunity.

Recent findings reveal unanticipated connections between the fields of lipid metabolism and immunology. They concern gammadelta and NKT cells, nonconventional T cell populations that do not recognize protein antigens and are involved in immunity against cancer, defense against infections, or in regulation of classical immune responses. In this review, we summarize data linking perturbations of apolipoprotein levels and nonconventional T cells with inflammatory processes such as autoimmune diseases or atherosclerosis. We integrate and discuss recent findings on the implication of apolipoproteins in antigen recognition by gammadelta and NKT cells, with emphasis on apolipoproteins A-I and E. These findings also provide indications that apolipoproteins influence antitumor immunosurveillance.

Animals↗
PubMed2004

Serine-threonine kinases and transcription factors active in signal transduction are detected at high levels of phosphorylation during mitosis in preimplantation embryos and trophoblast stem cells.

Serine-threonine kinases and transcription factors play important roles in the G1-S phase progression of the cell cycle. Assays that use quantitative fluorescence by immunocytochemical means, or that measure band strength during Western blot analysis, may have confused interpretations if the intention is to measure G1-S phase commitment of a small subpopulation of phosphorylated proteins, when a larger conversion of the same population of proteins can occur during late G2 and M phases. In mouse trophoblast stem cells (TSC), a human placental cell line (HTR), and/or mouse preimplantation embryos, 8/19 serine-threonine and tyrosine kinases, 3/8 transcription factors, and 8/14 phospho substrate and miscellaneous proteins were phosphorylated at higher levels in M phase than in interphase. Most phosphoproteins appeared to associate with the spindle complex during M phase, but one (p38MAPK) associated with the spindle pole and five (Cdx2, MEK1, 2, p27, and RSK1) associated with the DNA. Phosphorylation was detected throughout apparent metaphase, anaphase and telophase for some proteins, or for only one of these segments for others. The phosphorylation was from 2.1- to 6.2-fold higher during M phase compared with interphase. These data suggest that, when planning and interpreting quantitative data and perturbation experiments, consideration must be given to the role of serine-threonine kinases and transcription factors during decision making in M phase as well as in G1-S phase.

Animals↗
PubMed2004

Studies on the interaction of papain with human placental cystatin by UV, fluorescence and CD spectroscopy.

The interaction of activated papain with low molecular weight cystatin (Mr 12500) purified from human placenta has been studied. Analysis of inhibition of caesinolytic activity of papain by cystatin showed stoichiometry of 1:1. Kinetic studies gave an inhibition constant (K(i)) value of 5.5 x 10(-8) M and association rate constant (K(+1)) value of 3.4 x 10(4) (M(-1) s(-1)). All spectroscopic studies showed conformational changes in both papain and cystatin on formation of complex. The data suggest perturbation of environment of aromatic residues and change of their native structure and conformation thereby shedding light on the behaviour of cystatins, especially interaction of placental cystatin with thiol protease inhibitors.

Circular Dichroism↗
PubMed1990

Free-fatty acid inhibition of insulin binding, degradation, and action in isolated rat hepatocytes.

The effect of free fatty acids (FFAs) on insulin binding and action was investigated in isolated rat hepatocytes. Oleic acid (0.4 mM) added to the cells rapidly (within 45 min) reduced insulin binding and degradation (each by 45%; P less than 0.001, n = 7) without changing the apparent receptor affinity. The effect was concentration dependent; a half-maximal inhibitory effect occurred at 0.150 +/- 0.050 mM (mean +/- SE). Oleic acid exerted no effect on insulin binding in energy-depleted (KCN-treated) cells. Oleic, palmitic, stearic, palmitoleic, and eicosapentaenoic acids were equally effective in reducing insulin binding. FFA did not change insulin binding to partially purified insulin receptors, thus excluding a direct effect on the insulin receptor. Furthermore, binding to partially purified receptors from solubilized cells pretreated with 0.2 mM oleic acid was not changed, indicating the effect of FFA in intact cells is on the rate of receptor internalization and/or recycling. Concomitant with the effect on insulin binding, oleic acid elicited a concentration-dependent reduction in nonstimulated cellular [14C]aminoisobutyric acid uptake (AIB; 29 +/- 8%, P less than 0.05) and decreased the maximal effect of insulin (39 +/- 7%, P less than 0.05). Thus, in a concentration-dependent manner, different fatty acids can reduce the number of binding sites for insulin and the degradation of insulin by isolated liver cells. Basal and insulin-stimulated AIB transport was reduced, suggesting the presence of postbinding perturbations. These data suggest that FFA exerts an important modulating effect on insulin action in the liver.

Aminoisobutyric Acids↗
PubMed2000

Granulysin, a T cell product, kills bacteria by altering membrane permeability.

Granulysin, a protein located in the acidic granules of human NK cells and cytotoxic T cells, has antimicrobial activity against a broad spectrum of microbial pathogens. A predicted model generated from the nuclear magnetic resonance structure of a related protein, NK lysin, suggested that granulysin contains a four alpha helical bundle motif, with the alpha helices enriched for positively charged amino acids, including arginine and lysine residues. Denaturation of the polypeptide reduced the alpha helical content from 49 to 18% resulted in complete inhibition of antimicrobial activity. Chemical modification of the arginine, but not the lysine, residues also blocked the antimicrobial activity and interfered with the ability of granulysin to adhere to Escherichia coli and Mycobacterium tuberculosis. Granulysin increased the permeability of bacterial membranes, as judged by its ability to allow access of cytosolic ss-galactosidase to its impermeant substrate. By electron microscopy, granulysin triggered fluid accumulation in the periplasm of M. tuberculosis, consistent with osmotic perturbation. These data suggest that the ability of granulysin to kill microbial pathogens is dependent on direct interaction with the microbial cell wall and/or membrane, leading to increased permeability and lysis.

Amino Acid Sequence↗
PubMed2002

Molecular dosimetry and repair of N(2),3-ethenoguanine in rats exposed to vinyl chloride.

Although the DNA adducts of vinyl chloride (VC) have been well characterized, previous studies have used single concentrations of VC that are well above contemporary human exposures. This study examined the exposure response to VC in male Sprague Dawley rats with respect to the molecular dose of the promutagenic DNA adduct N(2),3-ethenoguanine (N(2),3-epsilonG). Adult rats were exposed by inhalation to 0, 10, 100, or 1100 ppm VC for 1 or 4 weeks (6 h/day, 5 days/week). Weanling rats were similarly exposed for 5 days. The amount of N(2),3-epsilonG in hepatocyte (HEP) and nonparenchymal cell (NPC) fractions obtained from the liver was measured with a sensitive immunoaffinity/gas chromatography/high-resolution mass spectrometry assay. Endogenous N(2),3-epsilonG was present in HEPs and NPCs from all unexposed rats. The exposure response to VC in each group and cell population was supralinear, with a linear increase from 0 to 100 ppm, and a plateau between 100 and 1100 ppm. There was no statistically significant difference in N(2),3-epsilonG concentrations between HEPs and NPCs in any adult exposure group, which suggests that factors other than adduct concentrations contribute to the particular susceptibility of NPCs to VC-induced carcinogenesis. The accumulation of N(2),3-epsilonG with respect to time was nearly linear in rats exposed to 600 ppm VC for 1, 2, 4, or 8 weeks (4 h/day, 5 days/week), and no repair of N(2),3-epsilonG was detected in rats exposed to VC for 4 weeks and allowed to recover for 1 week. N(2),3-epsilonG concentrations in HEPs from weanling rats were 2-3-fold greater than those in adult rats exposed for the same time. Higher adduct concentrations in young rats may contribute to their greater susceptibility to VC-induced hepatic angiosarcoma as well as their particular susceptibility to hepatocellular carcinoma. The molecular dosimetry of N(2),3-epsilonG in liver appears to be a sensitive and informative biomarker of genotoxic effect after exposure to VC. N(2),3-epsilonG was the predominant etheno adduct measured in vivo after exposure to VC, and the saturable nature of VC metabolism was reflected in its molecular dose. The relationships between endogenous N(2),3-epsilonG and that formed by low exposures to VC were demonstrated. Conclusions drawn from these exposures may be more relevant for risk assessment purposes than those drawn from high exposures where activation, detoxication, and repair pathways may be saturated or otherwise perturbed. These data are well suited for consideration in future risk assessments of VC that incorporate nontumor mode of action data.

Administration, Inhalation↗
PubMedDate not supplied

[S-N transition of the saccharide ring in B-form DNA].

A conformational transition of a single deoxyribose was analyzed in B-form trimers dA3:dT3 and dG3:dC3, both in the purine and pyrimidine chains. The main results were obtained for the duplexes with frozen ends, which could be extended by regular double helixes. The geometry of the central sugar ring in the duplexes may strongly deviate from the regular conformation. When deoxyribose changed its conformation in the central pyrimidine, the energy increase was proved to be less significant in comparison with that for purine. In the case of Thy, a decrease in pseudorotation angle P from 140 to 80 degrees causes the energy increase of 0.5 kcal/mol only, the barrier being 1.2 kcal/mol. The energy profile for Cyt has several local minima. The results of calculations were compared with numerous experimental data, they help to explain some NMR data. A perturbation of the duplex AAA:TTT structure caused by the thymine sugar ring transition, produces 5 degrees bend of the DNA axis directed toward adenines. We also investigated the influence of such conformational disturbance on the neighbouring base pairs, in particular the transition in the trimers with unfrozen ends.

DNA↗
PubMed1985

Depression and serotonin metabolism: rationale for neurotransmitter precursor treatment.

The authors review evidence suggesting that some depressed patients have disturbances in serotonin metabolism. Research supporting the serotonin hypothesis includes: cerebrospinal fluid studies; postmortem examination of neurotransmitters, their metabolites, and their receptors; platelet studies; neuropharmacologic data; neuroendocrine perturbations; and reports that serotonin precursor compounds (tryptophan and 5-hydroxytryptophan) may benefit some depressed patients. The authors conclude that better designed studies are needed to test whether serotonin precursor compounds have antidepressant properties.

5-Hydroxytryptophan↗
PubMed1986

NMR studies of pig gastric microsomal H+,K+-ATPase and phospholipid dynamics. Effects of ethanol perturbation.

The effects of ethanol on the gastric H+,K+-ATPase activity and the degree of mobility of various microsomal phospholipids were assessed using 31P and 1H NMR. This illuminated the role of lipid-protein association in the function of pig gastric microsomes. Treatment of gastric microsomes with 15% ethanol for 1 min at 37 degrees C inactivated the H+,K+-ATPase activity, which could largely be reconstituted by supplementation with phosphatidylcholine isolated from the gastric microsomes. Under similar conditions, the 1H NMR profile of the microsomal +N(CH3)3 choline moiety showed dramatic enhancement of peak intensity as well as a break point at 25 degrees C which was restored to the untreated control value after reconstitution. This break, together with the dramatic enhancement in the overall lipid profile, compared to the control and reconstituted microsomes, suggested a greater degree of freedom of movement of the microsomal lipids following ethanol perturbation. The data demonstrate the unique ability that a combined approach using 31P and 1H NMR holds as a noninvasive probe to study the structure-function relationship of biomembranes.

Adenosine Triphosphatases↗
PubMed1995

[Postpartum parvovirus B19-associated acute pure red cell aplasia and hemophagocytic syndrome].

A 30-year-old postpartum woman was admitted to our hospital because of progressive anemia, malaise, night sweating, headache and low grade fever which began 9 days after delivery (day 0). She had normocytic hypochromic anemia accompanied with marked decrease in reticulocytes. In addition, a temporary decrease in platelets and white blood cells especially neutrophils were observed. Bone marrow smears showed an apparent decrease in erythroid cells and the presence of giant proerythroblasts (1.2%) as well as hemophagocytes (1.2%). IgM and IgG antibody against human parvovirus B19 (HPV) was detected on day 22 of the disease although negative results were obtained on day 3. The presence of the virus in the blood on admission was confirmed by dot-blot analysis. Thus, this case was diagnosed as acute pure red cell aplasia and hemophagocytic syndrome caused by HPV infection. This patient had been given iron for iron deficiency anemia before delivery and the iron deficiency was still present after the episode of the present disease although the iron metabolism data was perturbed during the disease. These findings suggest that HPV could cause acute pure red cell aplasia not only in patients with hemolytic anemia but also in patients with iron deficiency anemia or after acute bleeding. Furthermore it is suggested that pancytopenia often observed on HPV infection could be at least partly caused by hemophagocytic syndrome.

Adult↗
PubMed1997

Overexpression of c-fos inhibits down-regulation of a cyclin-dependent kinase-2 inhibitor p27Kip1 in splenic B cells activated by surface Ig cross-linking.

Splenic B cells activated by surface Ig (sIg) cross-linking transiently express the c-fos gene within 0.5 h and then enter into S phase of the cell cycle within 48 h. To investigate a role of c-fos in cell cycle progression, we used splenic B cells from IFN-alphabeta-inducible c-fos transgenic mice (Mx-c-fos). In the absence of IFN, the cell cycle progression of Mx-c-fos B cells stimulated with anti-IgM Ab was similar to that in control B cells. The cell cycle was arrested in G1 phase when we added IFN to the culture within 12 h after anti-IgM Ab stimulation, suggesting that overexpression of c-fos until mid-G1 phase perturbs activation of the cell cycle regulatory machinery. In control B cells, cyclin E and cdk2 were induced within 24 to 48 h after stimulation, and this induction was accompanied by down-regulation of a cdk2 inhibitor p27Kip1. As a consequence of these activation processes, cdk2 kinase activity was induced in B cells in the late G1 phase. However, kinase activity was not detected in Mx-c-fos B cells, presumably because the down-regulation of p27 was perturbed. These data suggest that c-Fos can negatively control cell cycle regulatory machinery in sIg-stimulated B cells.

Animals↗
PubMed2001

Neutral pion threshold production at Q(2) = 0.05 GeV(2)/c(2) and chiral perturbation theory.

New data are presented on the p(e,e'p)pi(0) reaction at threshold at a four-momentum transfer of Q(2) = 0.05 GeV(2)/c(2). The data were taken with the three-spectrometer setup of the A1 Collaboration at the Mainz Microtron MAMI. The complete center of mass solid angle was covered up to a center of mass energy of 4 MeV above threshold. Combined with measurements at three different values of the virtual photon polarization epsilon, the structure functions sigma(T), sigma(L), sigma(TT), and sigma(TL) are determined. The results are compared with calculations in heavy baryon chiral perturbation theory and with a phenomenological model. The measured cross section is significantly smaller than both predictions.

Journal Article↗
PubMed2006

Effects of neuromuscular training on the reaction time and electromechanical delay of the peroneus longus muscle.

OBJECTIVE: To examine the influence of a 6-week neuromuscular training program on the electromechanical delay and reaction time of the peroneus longus muscle. DESIGN: A 2 x 2 pre-post factorial design. SETTING: Human performance research center biomechanics laboratory. PARTICIPANTS: Thirty-six healthy, physically active, college-age subjects were recruited for this study and 26 completed it. There were 5 men and 8 women in the treatment group (mean age +/- standard deviation, 21.9+/-2.1 y; height, 173.7+/-11.1cm; weight, 67.4+/-17.8 kg) and 6 men and 7 women in the control group (age, 21.8+/-2.3 y; height, 173.7+/-11.9 cm; weight, 70.8+/-19.4 kg). Subjects were not currently experiencing any lower-extremity pathology and had no history of injuries requiring treatment to either lower extremity. INTERVENTIONS: Subjects in the treatment group completed a 6-week neuromuscular training program involving various therapeutic exercises. Subjects in the control group were asked to continue their normal physical activity during the 6-week period. MAIN OUTCOME MEASURES: The electromechanical delay of the peroneus longus was determined by the onset of force contribution after artificial activation, as measured by electromyographic and forceplate data. Reaction time was measured after a perturbation during walking. Data were analyzed using two 2 x 2 analyses of covariance (covariate pretest score). Group (treatment, control) and sex (male, female) were between-subject factors. RESULTS: Neuromuscular training caused a decrease in reaction time to perturbation during walking compared with controls (F=4.030, P=.029), while there was a trend toward an increase in electromechanical delay (F=4.227, P=.052). There was no significant difference between sexes or the interaction of sex and treatment in either reaction time or electromechanical delay. CONCLUSIONS: The 6-week training program significantly reduced reaction time of the peroneus longus muscle in healthy subjects. Neuromuscular training may have a beneficial effect on improving dynamic restraint during activity.

Adult↗
PubMed2005

Ensembling local learners through multimodal perturbation.

Ensemble learning algorithms train multiple component learners and then combine their predictions. In order to generate a strong ensemble, the component learners should be with high accuracy as well as high diversity. A popularly used scheme in generating accurate but diverse component learners is to perturb the training data with resampling methods, such as the bootstrap sampling used in bagging. However, such a scheme is not very effective on local learners such as nearest-neighbor classifiers because a slight change in training data can hardly result in local learners with big differences. In this paper, a new ensemble algorithm named Filtered Attribute Subspace based Bagging with Injected Randomness (FASBIR) is proposed for building ensembles of local learners, which utilizes multimodal perturbation to help generate accurate but diverse component learners. In detail, FASBIR employs the perturbation on the training data with bootstrap sampling, the perturbation on the input attributes with attribute filtering and attribute subspace selection, and the perturbation on the learning parameters with randomly configured distance metrics. A large empirical study shows that FASBIR is effective in building ensembles of nearest-neighbor classifiers, whose performance is better than that of many other ensemble algorithms.

Algorithms↗
PubMed2004

Predicting genetic regulatory response using classification.

MOTIVATION: Studying gene regulatory mechanisms in simple model organisms through analysis of high-throughput genomic data has emerged as a central problem in computational biology. Most approaches in the literature have focused either on finding a few strong regulatory patterns or on learning descriptive models from training data. However, these approaches are not yet adequate for making accurate predictions about which genes will be up- or down-regulated in new or held-out experiments. By introducing a predictive methodology for this problem, we can use powerful tools from machine learning and assess the statistical significance of our predictions. RESULTS: We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular experiment based on (1) the presence of binding site subsequences ('motifs') in the gene's regulatory region and (2) the expression levels of regulators such as transcription factors in the experiment ('parents'). Thus, our learning task integrates two qualitatively different data sources: genome-wide cDNA microarray data across multiple perturbation and mutant experiments along with motif profile data from regulatory sequences. We convert the regression task of predicting real-valued gene expression measurements to a classification task of predicting +1 and -1 labels, corresponding to up- and down-regulation beyond the levels of biological and measurement noise in microarray measurements. The learning algorithm employed is boosting with a margin-based generalization of decision trees, alternating decision trees. This large-margin classifier is sufficiently flexible to allow complex logical functions, yet sufficiently simple to give insight into the combinatorial mechanisms of gene regulation. We observe encouraging prediction accuracy on experiments based on the Gasch S.cerevisiae dataset, and we show that we can accurately predict up- and down-regulation on held-out experiments. We also show how to extract significant regulators, motifs and motif-regulator pairs from the learned models for various stress responses. Our method thus provides predictive hypotheses, suggests biological experiments, and provides interpretable insight into the structure of genetic regulatory networks. AVAILABILITY: The MLJava package is available upon request to the authors. Supplementary: Additional results are available from http://www.cs.columbia.edu/compbio/geneclass

Binding Sites↗
PubMed1996

Pitfalls in the measurement of bone mineral density by dual energy x-ray absorptiometry.

STUDY DESIGN: Fifty-three human thoracic and lumbar vertebrae were analyzed by dual energy x-ray absorptiomety to obtain projectional (g/cm2) and volumetric (g/cm3) bone mineral density. OBJECTIVES: To determine the effect of volume on the measurement of bone mineral density by DEXA. SUMMARY OF BACKGROUND DATA: Despite the widespread use of dual energy x-ray absorptiomety to measure bone mineral density expressed as grams per projectional unit area (g/cm2), the effect of volume has been ignored in many published biomechanical studies. METHODS: Projectional bone mineral density (g/cm2) of fifty-three human vertebrae was obtained by dual energy x-ray absorptiometry measurement. This was compared to bone mineral density expressed as grams per unit volume. RESULTS: Many specimens with near equal projectional bone mineral density were demonstrated to have significantly different true densities when measured by dual energy x-ray absorptiomety in grams per unit volume. The difference in true bone mineral density for these specimens ranged from 24.1% to 139%. CONCLUSION: The effect of volume on bone mineral density data based on projectional areas can cause very significant perturbations of the data in biomechanical studies.

Absorptiometry, Photon↗
PubMed1992

[Interpretation of experimental data in the presence of accidental perturbations: characterization of the bladder].

Some tests are subject to the influence of a special kind of "irreducible" effects which do not satisfy the Central Limit Theorem of statistics, even though they show no systematic character or tendency. These effects especially present when physiological experiments are concerned "in vivo". In such the lack of specific methods to reduce these effects brings about the necessity of special case in minimizing the loss of information. Contained in the experimental data as well as the accumulation of useless information. Recent work has suggested the extensive use of several indexes derived from combination of available variables and their respective mathematic correlation. The information obtained by following this methodology has the character of "working hypothesis" so it needs many favorable confirmation to assess its reliability. It is convenient to analyze a large number of relations in order to emphasize the concordant effects and discord the others. In order to obtain some preliminary indication of the reliability of this procedure we have analyzed some CMG curves in prostatic and non-prostatic subject. The final slope of the curves (urge point) t = dP/dVr has been adapted as an index of the "elasticity" of the bladder; it was compared with the filling volume, the muscular volume and their ratio, i.e. with a geometric index of the bladder shape. The correlation show that the index t can, to some extent significantly represent the mechanical behaviour of the bladder in its physiological condition or when there is a partial obstruction of urine deflection.(ABSTRACT TRUNCATED AT 250 WORDS)

Artifacts↗