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Results for “Correlation analysis”

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At least 199 records · Page 11Linked to original sources

PubMed2002

Conditional cross-correlation analysis of thalamocortical neurotransmission.

We developed a method to quantify the probability of a target neuron discharge following synchronous or asynchronous discharges among a pair of reference neurons. To illustrate this method, we simultaneously recorded three neurons having overlapping receptive fields in the somatosensory system: two reference neurons in the thalamic ventrobasal complex and one target neuron in the secondary somatosensory (SII) cortex. Our results show that focal cutaneous stimulation elicits synchronized discharges among thalamic neurons having similar place and submodality properties. Conditional cross-correlation analysis of the reference and target spike trains indicates that thalamic synchronization increases cortical responsiveness. This result suggests that neuronal synchronization plays a critical role in transmitting sensory information from thalamus to the cerebral cortex.

Algorithms↗

PubMed1991

Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels.

Molecular dynamics simulations have been done on a system consisting of the polypeptide membrane channel former gramicidin, plus water molecules in the channel and caps of waters at the two ends of the channel. In the absence of explicit simulation of the surrounding membrane, the helical form of the channel was maintained by artificial restraints on the peptide motion. The characteristic time constant of the artificial restraint was varied to assess the effect of the restraints on the channel structure and water motions. Time-correlation analysis was done on the motions of individual channel waters and on the motions of the center of mass of the channel waters. It is found that individual water molecules confined in the channel execute higher frequency motions than bulk water, for all degrees of channel peptide restraint. The center-of-mass motion of the chain of channel waters (which is the motion that is critical for transmembrane transport, due to the mandatory single filing of water in the channel) does not exhibit these higher frequency motions. The mobility of the water chain is dramatically reduced by holding the channel rigid. Thus permeation through the channel is not like flow through a rigid pipe; rather permeation is facilitated by peptide motion. For the looser restraints we used, the mobility of the water chain was not very much affected by the degree of restraint. Depending on which set of experiments is considered, the computed mobility of our water chain in the flexible channel is four to twenty times too high to account for the experimentally measured resistance of the gramicidin channel to water flow. From this result it appears likely that the peptide motions of an actual gramicidin channel embedded in a lipid membrane may be more restrained than in our flexible channel model, and that these restraints may be a significant modulator of channel permeability. For the completely rigid channel model the "trapping" of the water molecules in preferred positions throughout the molecular dynamics run precludes a reasonable assessment of mobility, but it seems to be quite low.

Gramicidin↗

PubMed2005

Correlational analysis of proteins and nonmetallic nanoparticles in a deep-nulling microscope.

We present a method for label-free microscopic analysis of nonmetallic nanoparticles such as biopolymers or technical polymers diffusing freely in an aqueous environment. We demonstrate the principal feasibility of the approach with first measurements of 20-200 nm sized polystyrene spheres and of the approximately 10 nm protein complex Photosystem I (PS I) of Thermosynechococcus elongatus. The approach is based on the combination of a microscope setup with a deep-nulling interferometer for measuring minute refractive index changes or absorptions in the focal area of the microscope. It is possible to obtain transient nulls in a microscope setup on the order of 10(-5), corresponding to optical pathway differences of less than 0.6 nm and to stabilize the nulls to about 5.10(-4). With this level of stabilization it is possible to perform a fast (1 s) correlational analysis of aqueous solutions containing the protein complex PS I or 20 nm spheres and to detect in real time single diffusional transits of larger nanospheres through the focal area of the microscope. A modulated heating of the samples in the microscope focus is not necessary for detection. The interferometer correlation data correspond well to conventional two-photon excited fluorescence correlation (FCS) data measured in the same setup, providing evidence that the detection volumes are of a similar size (approximately 200 nm). We also conducted first nulling experiments using coherent near-field sources of about 30 nm diameter. Theoretical considerations indicate that this combination with nanometric near-field sources will even allow label-free single-protein analysis.

Bacterial Proteins↗

PubMed1990

Stimulus-Dependent Neuronal Oscillations in Cat Visual Cortex: Inter-Columnar Interaction as Determined by Cross-Correlation Analysis.

We have demonstrated previously that neurons in cat striate cortex, in response to their preferred stimuli, exhibit oscillatory responses in a frequency range of 40 - 60 Hz. Recently, we obtained evidence that such oscillatory responses can synchronize across columns. We have now performed an extensive analysis of this phenomenon for both unit and field potential responses. In addition, we studied the stimulus conditions leading to intercolumnar synchronization. We recorded both multi-unit activity and local field potentials from area 17 of adult cats with arrays of several electrodes. Interelectrode distances ranged from 0.4 to 12 mm. For all pairs of unit (n=200) and field potential (n=174) recordings, we computed auto- and cross-correlation functions. The modulation of the correlograms was quantified by fitting a damped sine wave (Gabor) function to the data. Cross-correlation analysis of the unit data revealed that in 90 out of 200 cases the recorded cells established a constant phase-relationship of their oscillatory responses. This occurred, on average, with no phase difference. If the receptive fields were nonoverlapping, we observed a synchronization primarily between cells with similar orientation preferences. Cells with overlapping receptive fields also showed a high incidence of synchronization if their orientation preferences were different. In this latter group, synchronization occurred even in cases where the stimulus was optimal for only one of the recording sites. Under conditions of monocular instead of binocular stimulation the oscillatory modulation of the responses was attenuated, but the cross-correlogram still indicated a significant interaction. Similar effects were seen with the application of stationary instead of moving stimuli. A synchronization of oscillatory field potential responses was observed in 136 out of 174 paired recordings. At all distances investigated, the probability of synchronization of field potential responses was independent of the orientation preferences of the cells. However, the strength of interaction decreased with increasing spatial separation. Control experiments showed that the synchronization of field potential responses was not due to volume conduction. The results demonstrate that oscillatory responses at separate cortical sites can transiently synchronize. The probability and strength of synchronization are dependent on the spatial separation of the recorded cells and their orientation preferences. In addition, the cross-columnar synchronization is influenced by features of the visual stimulus. It is suggested that this synchronization provides a mechanism for the formation of neuronal assemblies in the visual cortex.

Journal Article↗

PubMedDate not supplied

Enhancement of hidden structures of early skin fibrosis using polarization degree patterns and Pearson correlation analysis.

The skin of athymic nude mice is irradiated with a single dose of x-ray irradiation that initiated fibrosis. Digital photographs of the irradiated mice are taken by illuminating the mouse skin with linearly polarized probe light of 650 nm. The specific pattern of the surface distribution of the degree of polarization enables the detection of initial skin fibrosis structures that were not visually apparent. Data processing of the raw spatial distributions of the degree of polarization based on Fourier filtering of the high-frequency noise improves subjective perception of the revealed structure in the images. In addition, Pearson correlation analysis provides information about skin structural size and directionality.

Algorithms↗

PubMed2003

Novel nonparametric approach to canonical correlation analysis with applications to low CNR functional MRI data.

Detection of activation in functional MRI (fMRI) is often complicated by the low contrast-to-noise ratio (CNR) in the data. The primary source of the difficulty is the fact that for activities that are subtle the signal can be hidden inside the inherent noise in the data. Classical univariate methods based on t-test or F-test are susceptible to noise, as they fail to harness systematic correlations in evoked responses within neighboring voxels. Here the power of a multivariate statistical analysis tool known as canonical correlation analysis (CCA) in fMRI studies is demonstrated where the CNR is low. As a further illustration of the power of the method, a comparative study of CCA and ordinary correlation analysis using simulated data under various noise levels is also performed. A novel nonparametric approach is introduced to calculate the P-values from the distribution of the complicated test statistic. The circumstances under which CCA is a better performer as well as when it is not the case are discussed. As an example, this method is applied to detect hippocampal activation from memory-related tasks.

Adult↗

PubMed1996

Third-order reverse correlation analysis of muscle spindle primary afferent fiber responses to random muscle stretch.

The response of primary muscle spindle afferent fibers to muscle stretch is nonlinear. Now spindle responses (trains of action potentials) to band-limited Gaussian white noise length perturbations of the gastrocnemius muscles (input signal) are described in cats. The input noise upper cutoff frequency was clearly above the frequency range of physiological length changes in cat hindleg muscles. The input-output relation was analyzed by means of peri-spike averages (PSAs), which could be shown to correspond to the kernels of Wiener's white noise approach to systems identification. The present approach (the reverse correlation analysis) was applied up to the third order. An experiment consisted of two recordings: one (the source recording) to determine PSAs and the other (the test recording) to provide an input signal for predicting responses. The predictions of different orders were compared with the actual neuronal response (the observation) of the test recording. Four different approximation procedures were developed to adapt prediction and observation and to determine weighting factors for the predictions of different orders. The approximations also yielded the value of the power density P of the input noise signal: at a variety of stimulus parameters, P from approximations had the same magnitude as P determined directly from the input signal amplitude spectrum. The prediction of a sequence of action potentials improved the higher the order of components. 37 of 42 action potentials of a test recording (the observation) could be confidently predicted from PSAs or kernels. Compared with the size of the linear first-order prediction curve, the relative sizes of the second and third-order prediction curves were: 1.0:0.47:0.26.

Action Potentials↗

PubMedDate not supplied

Correlation analysis of alveolar macrophage cytochemical parameters in smoking and pulmonary oncology.

Cytochemical examination of alveolar macrophages (AM) obtained by bronchoalveolar lavage (BAL) was performed in healthy volunteers (11 non-smokers and 11 smokers) and in 9 patients with squamous lung carcinoma (all of them smokers or ex-smokers) in order to analyze its peculiarities related to the smoking habit and to lung malignancy. Assessment of non-specific esterases: alpha-naphthyl acetate esterase (ANAE) and butyrate esterase (BUT), chloroacetate esterase (CHL), acid phosphatase (AcP), intracellular glycogen (PAS reaction), lipids (Sudan black B reaction-SBB) and iron (Perl's reaction) was performed by a semiquantitative cytochemical method (1). A significant correlation was obtained between BUT and stage of squamous lung carcinoma (varying between I and IV) (r = 0.52, p < 0.05). There was a correlation between BUT and Perl's in healthy controls (r = 0.76, p < 0.05). The same type of correlation was observed in control smokers (r = 0.64, p < 0.05), in addition to a correlation between CHL and AcP (r = 0.69, p < 0.05). There was no significant BUT/Perl's correlation in patients with squamous cell lung carcinoma (r = 0.23, p > 0.05), but significant AcP/CHL correlation as was observed in control smokers (r = 0.73, p < 0.05), and a "new" type of correlation was shown to exist between ANAE and SBB (r = 0.77, p < 0.05). In spite of the unresolved nature of lung cancer, correlation analysis of cytochemical parameters in AM might have an important part in the analysis of their relative contribution to the development of smoking-related disorders and lung malignancies.

Acid Phosphatase↗

PubMed2001

Postsynaptic dorsal column and cuneate neurons in raccoon: comparison of response properties and cross-correlation analysis.

The responses of 111 postsynaptic dorsal column (PSDC) neurons in the cervical spinal cord and 51 cuneate neurons with receptive fields on the glabrous skin of the forepaw were studied in anesthetized raccoons using extracellular recording techniques. The PSDC neurons had larger receptive fields than the cuneate neurons, but in both groups the fields never extended onto hairy skin. PSDC and cuneate neurons had approximately the same mean latency to electrical stimulation of the receptive field, but PSDC neurons had significantly lower thresholds. The majority of both PSDC and cuneate neurons also responded to electrical stimulation of an adjacent digit, even though they did not respond to mechanical stimulation of that digit. Cross-correlation analysis of the activity of 51 pairs of PSDC and cuneate neurons recorded simultaneously revealed a significant interaction in 26 pairs during spontaneous activity. In 20 of these neuron pairs, the probability that the cuneate neuron would fire was greater after the PSDC neuron had fired (suggesting a spinocuneate interaction), five pairs showed an interaction in the opposite (cuneospinal) direction, and one pair had a significant inhibitory interaction. These interactions occurred more often when the receptive fields of the two neurons were overlapping than when their fields were on adjacent digits. Frequency response analysis revealed greater coherence for those pairs showing a spinocuneate interaction than for those with a cuneospinal interaction. These results support the hypothesis that the PSDC system exerts a tonic facilitatory effect on cuneate neurons and that there may be some somatotopic organization to the interactions. However, the similar response latencies of the two groups of neurons makes it unlikely that PSDC neurons could contribute to the rapid initial processing of cutaneous information by the cuneate nucleus.

Action Potentials↗

PubMed2005

Canonical correlation analysis for data reduction in data mining applied to predictive models for breast cancer recurrence.

Data mining methods can be used for extracting specific medical knowledge such as important predictors for recurrence of breast cancer in pertinent data material. However, when there is a huge quantity of variables in the data material it is first necessary to identify and select important variables. In this study we present a preprocessing method for selecting important variables in a dataset prior to building a predictive model.In the dataset, data from 5787 female patients were analysed. To cover more predictors and obtain a better assessment of the outcomes, data were retrieved from three different registers: the regional breast cancer, tumour markers, and cause of death registers. After retrieving information about selected predictors and outcomes from the different registers, the raw data were cleaned by running different logical rules. Thereafter, domain experts selected predictors assumed to be important regarding recurrence of breast cancer. After that, Canonical Correlation Analysis (CCA) was applied as a dimension reduction technique to preserve the character of the original data.Artificial Neural Network (ANN) was applied to the resulting dataset for two different analyses with the same settings. Performance of the predictive models was confirmed by ten-fold cross validation. The results showed an increase in the accuracy of the prediction and reduction of the mean absolute error.

Breast Neoplasms↗

PubMed2004

[Correlation analysis between single nucleotide polymorphism of the leptin receptor intron 8 and fatness traits in chickens].

Leptin receptor plays an important role in leptin functioning signal transduction and it may have direct effects on the deposition of adipose tissues and the body weight, the leptin receptor (OBR) gene, therefore, can be considered as a candidate gene in the study of fat deposition of the chicken. The function of OBR gene has been intensively studied in mammals, but study of OBR gene in the chicken is still rare. In this paper, the NEAU divergent selection broiler lines for abdominal fat were used. Body weight and fatness traits were measured in the sixth generation broiler population of the two lines at 7 week of age. Two pairs of primers for intron 8 of OBR gene were designed according to the database of chicken genomic sequence (Accession No. AF222783). The SNP was detected by DNA sequencing, and PCR-SSCP method was then developed to screen the population. The correlation analysis between the polymorphisms of the intron 8 of OBR gene and growth and fatness traits in the population was carried out using the appropriate statistical model. Two SNPs were found in the population. Those were T500C and G659A. The least square analysis showed that BB genotype birds had significant higher (P < 0.05) abdominal fat weight and percentage of abdominal fat than AA and AB genotype birds, and AA genotype birds had significant lower (P < 0.05) weights of livers than AB and BB genotype birds at the same time. From these results we can putatively drew the conclusion that OBR gene may be a major gene to affect the fatness traits or linked to the major gene, and the two polymorphisms found in OBR gene intron 8 region could be used to select the chicken for low abdominal fat in molecular marker-assisted selection programs.

Adipose Tissue↗

PubMed2006

Correlation analysis between single-nucleotide polymorphism of malate dehydrogenase gene 5'-flanking region and growth and body composition traits in chicken.

Malate dehydrogenase (MD) is a key enzyme that plays an important role in energy metabolism. It catalyzes the oxidative decarboxylation of L-malate to yield CO2 and pyruvate, while simultaneously generating NADPH from NADP+. The NADPH generated can be utilized in de novo synthesis of palmitate, which is the precursor molecule for the formation of other long-chain fatty acids. And high levels of MD will also activate muscle development. The current study was designed to investigate the effects of MD gene on growth and body-composition traits in chicken. The eighth generation population of Northeast Agricultural University broiler lines divergently selected for its abdominal fat and Northeast Agricultural University F2 resource population were used in the research. Polymorphisms were detected by DNA sequencing and PCR-RFLP method was then developed to screen the population. A single mutation at the position of the 235 bp (Accession No. U49693) of MD 5'-flanking region was found. The correlation analysis between the polymorphism of the MD gene and growth and body composition traits was carried out using the appropriate statistic model. Least-square analysis showed that the BB genotype birds had much higher pectoralis major weight and percentage of pectoralis major than AA genotype birds (P<0.05). The abdominal fat weight, percentage of abdominal fat, the liver weight and percentage of liver weight of the AA genotype birds were much higher than those of BB genotype birds (P<0.05). These results indicate that MD gene is the major gene or is linked to the major gene that affects the growth and body composition traits in chicken.

5' Flanking Region↗

PubMed1992

Examination of fungi in domestic interiors by using factor analysis: correlations and associations with home factors.

Factor analysis was utilized to investigate correlations among airborne microorganisms collected with Andersen samplers from homes in Topeka, Kans., during the winter of 1987 to 1988. The factors derived were used to relate microbial concentrations with categorical, questionnaire-derived descriptions of housing conditions. This approach successfully identified groups of common aboveground decay fungi including Cladosporium, Alternaria, Epicoccum, and Aureobasidium spp. The common soil fungi Aspergillus and Penicillium spp. were also separated as a group. These previously known ecological groupings were confirmed with air sampling data by a quantitative evaluation technique. The aboveground decay fungi sampled indoors in winter were present at relatively high concentrations in homes with gas stoves for cooking, suggesting a possible association between these fungi and increased humidity from the combustion process. Elevated concentrations of the soil fungi were significantly (P = 0.05) associated with the dirt floor, crawl-space type of basement. Elevated concentrations of water-requiring fungi, such as Fusarium spp., were shown to be associated with water collection in domestic interiors. Also, elevated mean concentrations for the group of fungi including Cladosporium, Epicoccum, Aureobasidium, and yeast spp. were found to be associated (P = 0.03) with symptoms reported on a health questionnaire. This finding was consistent with our previous study of associations between respiratory health and airborne microorganisms by univariate logistic regression analysis.

Air Microbiology↗

PubMed2003

2D-IR correlation analysis of deteriorative process of traditional Chinese medicine 'Qing Kai Ling' injection.

The traditional Chinese medicine 'Qing Kai Ling' injection after deterioration is distinguished from the original formulation using Fourier-transform infrared spectroscopy (FTIR) and two-dimensional correlation infrared spectroscopy (2D-IR). The IR spectra of the injections before and after deterioration are so similar, that it is very difficult to distinguish them by using the conventional approach. However, the higher spectral resolution and more structural information provided by 2D-IR analysis makes the identification possible. According to the results of 2D correlation analysis, the band at 1611 cm(-1) in IR spectra, in fact, consists of the overlap of three bands at 1572, 1667 and 1729 cm(-1), which are assigned to the alkaloids (heterocyclic compounds), flavone derivatives, and carbonyl compounds in the injection, respectively. Interestingly, the autopeak at 1667 cm(-1) disappears in synchronous spectrum of the deteriorated 'Qing Kai Ling' injection. It is suggested that the deterioration of the injection in air at room temperature be due to the oxidation of the flavone compounds mainly. As all intensities of the correlation peaks involved with the band in 1059 cm(-1) decrease greatly, it is assigned to the thermal decomposition of the glucoside components. Hence, it can conclude that the oxidation of the flavone compounds and the decomposition of the glucoside components are some of the main causes concerning to the deterioration of 'Qing Kai Ling' injection at ambient temperature. Thus, the 2D-correlation analysis provides a powerful method for the quality control of the traditional Chinese medicine injection.

Drug Stability↗

PubMed2004

A primer on the study of transitory dynamics in ecological series using the scale-dependent correlation analysis.

Here we describe a practical, step-by-step primer to scale-dependent correlation (SDC) analysis. The analysis of transitory processes is an important but often neglected topic in ecological studies because only a few statistical techniques appear to detect temporary features accurately enough. We introduce here the SDC analysis, a statistical and graphical method to study transitory processes at any temporal or spatial scale. SDC analysis, thanks to the combination of conventional procedures and simple well-known statistical techniques, becomes an improved time-domain analogue of wavelet analysis. We use several simple synthetic series to describe the method, a more complex example, full of transitory features, to compare SDC and wavelet analysis, and finally we analyze some selected ecological series to illustrate the methodology. The SDC analysis of time series of copepod abundances in the North Sea indicates that ENSO primarily is the main climatic driver of short-term changes in population dynamics. SDC also uncovers some long-term, unexpected features in the population. Similarly, the SDC analysis of Nicholson's blowflies data locates where the proposed models fail and provides new insights about the mechanism that drives the apparent vanishing of the population cycle during the second half of the series.

Animals↗

PubMed1996

Quantitative structure-activity analysis correlating Ras/Raf interaction in vitro to Raf activation in vivo.

Binding of Ras to c-Raf-1 is a pivotal step of many mitogenic signalling pathways. Based on the recent crystal structure of the complex of Rap1A with the Ras-binding domain of Raf, mutations were introduced in c-Raf-1 and their effects on Ras/Raf binding affinity in vitro and Ras/Raf regulated gene expression in vivo were analysed. Our data reveal an empirical semilogarithmic correlation between dissociation constants and Raf-induced gene activity. The functional epitope that primarily determines binding affinity consists of residues Gln 66, Lys 84 and Arg 89 in Raf. This quantitative structure-activity investigation may provide a general approach to correlate structure-guided biochemical analysis with biological function of protein-protein interactions.

Amino Acid Sequence↗

PubMed1992

[Correlation analysis between plasma atrial natriuretic peptide and cardiac function in blood deficiency syndrome].

The function of ANP in the cardiovascular regulation is very similar with the TCM theory of "the Heart governs blood circulation". Using the method of cardiac impedance to check cardiac output and the method of radioimmunoassay (RIA) to check plasma ANP, the result showed that in the status of Blood Deficiency Syndrome, cardiac function was impaired, there were reduced kinemia and stroke volume, as well as markedly raised plasma ANP and peripheral resistance. The above-mentioned indexes were significantly different from those of normal group (P < 0.01). Using multivariate regression analysis, cardiac output was negatively correlated with the plasma ANP (P < 0.05). 23 cases with Blood Deficiency Syndrome showed normal hemoglobin, but an evidently changed cardiac output and plasma ANP were closely related with the level of the Blood Deficiency. Both parameters might serve as the objective basis to reflect the level of Blood Deficiency to facilitate the clinical diagnosis of the patient.

Adult↗

PubMed2001

Stereochemical control factors in the Hantzsch thiazole synthesis: a Hammett substitution correlation analysis.

[reaction--see text] It is possible to correlate the distribution of stereochemical products produced during a Hantzsch thiazole synthesis according to the Hammett free-energy equation. This analysis confirms the presumed control of the rate of epimerization during thiazole formation due to stabilization of a cationic transition state intermediate during dehydration of the thiazoline ring system. In the chemical system under study, the stereochemical outcome of the reaction also appears to occur according to a kinetically controlled protonation of a thiazoline tautomer.

Journal Article↗