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PubMed1979

Spatial firing patterns of auditory neuron network modelling by computer simulation.

This communication examines, in digital computer simulated network, input signals and response patterns established at excitatory neurons' level i.e. the membrane potential of neuron soma. It is restricted to spatial patterns of the auditory neuron networks and time factor for nervous conduction and transmission is neglected compared with long maintained membrane potentials of neuron somas. The model analyzes the change in the spatial patterns of the membrane potential in the two dimensional networks of the auditory system. In order to evaluate the contribution of the various parameters, it is started that the simplest model has only one parameter, lateral inhibition. The other parameters are then added, one at a time, to successive models. The lateral inhibition is a necessary condition in the auditory nervous system if any sharpening of the response areas in the single neurons is to occur. A necessary condition for the validity of the model is that is should be applicable to the other senses such as vision and chemical patterns, taste. The threshold feature of auditory neurons aids in producing a sharpening in the neuron of the auditory relay nuclei. It does this clipping the spatial response patterns in one dimensional arrays of excitatory neurons. Recurrent inhibition seems a necessary condition in the sensory nervous system that any kinds of input signals are to be preserved over a wide range of stimulus intensity. In other words, this network has a wide dynamic range against any kinds of input signals. A simple self-recurrent negative feedback does not contribute to the sharpening, but more complex socalled averaged type does. A neuron network is capable of responding stably to stimuli with a wide range of intensity and with any kind of spatial patterns if there is a simple negative feedback mechanism. When there is no negative feedback, input signals soon disappear or saturate in the neuron network. Therefore, recurrent inhibition is the most important mechanism. Spontaneous activity appears to aid in the sharpening by providing a kind of contrast, that is by reducting the amount of activity in neurons adjacent to the excitatory area. Moreover, the effect of spontaneous activity in the model seems to make repples around the excitatory area and suggests that an introduction of activity at any stage of the networks, from whatever source for example reticulum formation and thalamus, might appreciably alter the response patterns at subsequent neuron network. This suggests that the mechanism of the consciousness that might be controlled by the thalamus and or reticular formation. These two dimensional neuron networks may be expanded to three dimensional neuron networks. The former might simulate the auditory nervous system while the latter might simulate the visual system.

Animals↗

PubMed2005

Nonlinear optical studies of heme protein dynamics: implications for proteins as hybrid states of matter.

Protein structure is fundamentally related to function. However, static structures alone are insufficient to understand how a protein works. Dynamics play an equally important role. Given that proteins are highly associated aperiodic systems, it may be expected that protein dynamics would follow glass-like dynamics. However, protein functions occur on time scales orders of magnitude faster than the time scales typically associated with glassy systems. It is becoming clear that the reaction forces driving functions do not sample entirely the large number of configurations available to a protein but are highly directed along an optimized pathway. Could there be any correlation between specific topological features in protein structures and dynamics that leads to strongly correlated atomic displacements in the dynamical response to a perturbation? This review will try to provide an answer by focusing upon recent nonlinear optical studies with the aim of directly observing functionally important protein motions over the entire dynamic range of the protein response function. The specific system chosen is photoinduced dynamics of ligand dissociation at the active site in heme proteins, with myoglobin serving as the simplest model system. The energetics and nuclear motions from the very earliest events involved in bond breaking on the femtosecond time scale all the way out to ligand escape and bimolecular rebinding on the microsecond and millisecond time scale have been mapped out. The picture that is emerging is that the system consists of strongly coupled motions from the very instant the bond breaks at the active site that cascade into low frequency collective modes specific to the protein structure. It is this coupling that imparts the ability of a protein to function on time scales more commensurate with liquids while simultaneously conserving structural integrity akin to solids.

Binding Sites↗

PubMed2004

Stable isotopic characterization of active pharmaceutical ingredients.

Stable isotopic characterization or "fingerprinting" of active pharmaceutical ingredients (APIs) is a highly-specific means of defining the provenance of these pharmaceutical materials. The isotopic analysts in this study were provided with 20 blind samples of four APIs (tropicamide, hydrocortisone, quinine HCL, and tryptophan) from one-to-five production batch(es) from one-to-five manufacturer(s). Only the chemical identity of the APIs was initially provided to the isotopic analysts. Depending on the API chemical composition, isotopic ratios of either three or four elements (13C/12C, 15N/14N, 18O/16O, and/or D/H) were measured by either elemental analyzer/isotope ratio mass spectrometry (EA/IRMS: carbon (delta13C) and nitrogen (delta15N)) or by thermal conversion-EA/IRMS (TCEA/IRMS; hydrogen (deltaD) and oxygen (delta15N)); in all cases, the isotopic results are reported in the standard delta-notation which represents part-per-thousand () variations from the isotopic ratios of international standards. The stable isotopic analyses of the four suites of APIs spanned broad ranges in absolute value (deltadelta) and in estimated specificity (a product of dynamic ranges (DR, unitless)--note that these are upper limits of specificity because some of these isotope values may be partially interdependent). The five samples of tropicamide from one production batch and one manufacturer demonstrated the narrowest ranges (deltadelta13C=0.13 ; deltadelta15N=0.52 ; deltadelta18O=0.24 ; deltadeltaD=2.8 ) and the smallest specificity of 1:30.9. By contrast, the five samples of tryptophan that came from five separate manufacturers had some of the widest isotopic ranges observed (deltadelta13C=21.32 ; deltadelta15N=5.26 ; deltadelta18O=22.07 ; deltadeltaD=55.3 ) and had the largest specificity of 1:19.6 x 10(6). The isotopic provenance of the four suites of APIs readily emerged from bivariate plots of selected isotope ratios, particularly deltaD versus delta18O.

Carbon Isotopes↗

PubMed2004

Real-time computation at the edge of chaos in recurrent neural networks.

Depending on the connectivity, recurrent networks of simple computational units can show very different types of dynamics, ranging from totally ordered to chaotic. We analyze how the type of dynamics (ordered or chaotic) exhibited by randomly connected networks of threshold gates driven by a time-varying input signal depends on the parameters describing the distribution of the connectivity matrix. In particular, we calculate the critical boundary in parameter space where the transition from ordered to chaotic dynamics takes place. Employing a recently developed framework for analyzing real-time computations, we show that only near the critical boundary can such networks perform complex computations on time series. Hence, this result strongly supports conjectures that dynamical systems that are capable of doing complex computational tasks should operate near the edge of chaos, that is, the transition from ordered to chaotic dynamics.

Animals↗

PubMed2003

Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system.

BACKGROUND: With the invention of the DNA chip, genome-wide analysis is now a reality. Unfortunately, solid-phase detection systems such as the DNA chip suffer from a narrow range in quantification and sensitivity. Today the best methodology for sensitive, wide dynamic range quantification and genotyping of nucleic acids is real-time PCR. However, multiplexed real-time PCR technologies require complicated and costly design and manufacturing of separate detection probes for each new target. METHODS: We developed a novel real-time PCR technology that uses universal energy transfer probes constructed from An Expanded Genetic Information System (AEGIS) for both quantification and genotyping analyses. RESULTS: RNA quantification by reverse transcription-PCR was linear over four orders of magnitude for the simultaneous analysis of beta-actin messenger RNA and 18S ribosomal RNA. A single trial validation study of 176 previously genotyped clinical specimens was performed by endpoint analysis for factor V Leiden and prothrombin 20210A mutation detection. There was concordance for 173 samples between the genotyping results from Invader tests and the AEGIS universal energy transfer probe system for both factor V Leiden and prothrombin G20210A. Two prothrombin and one factor V sample gave indeterminate results (no calls). CONCLUSION: The AEGIS universal probe system allows for rapid development of PCR assays for nucleic acid quantification and genotyping.

Actins↗

PubMed2004

Spike generator limits efficiency of information transfer in a retinal ganglion cell.

The quality of the signal a retinal ganglion cell transmits to the brain is important for preception because it sets the minimum detectable stimulus. The ganglion cell converts graded potentials into a spike train with a selective filter but in the process adds noise. To explore how efficiently information is transferred to spikes, we measured contrast detection threshold and increment threshold from graded potential and spike responses of brisk-transient ganglion cells. Intracellular responses to a spot flashed over the receptive field center of the cell were recorded in an intact mammalian retina maintained in vitro at 37 degrees C. Thresholds were measured in a single-interval forced-choice procedure with an ideal observer. The graded potential gave a detection threshold of 1.5% contrast, whereas spikes gave 3.8%. The graded potential also gave increment thresholds approximately twofold lower and carried approximately 60% more gray levels. Increment threshold "dipped" below the detection threshold at a low contrast (<5%) but increased rapidly at higher contrasts. The magnitude of the "dipper" for both graded potential and spikes could be predicted from a threshold nonlinearity in the responses. Depolarization of the cell by current injection reduced the detection threshold for spikes but also reduced the range of contrasts they can transmit. This suggests that contrast sensitivity and dynamic range are related in an essential trade-off.

Action Potentials↗

PubMed2006

Bayesian hierarchical model for correcting signal saturation in microarrays using pixel intensities.

Pixel saturation occurs when the pixel intensity exceeds the scanner upper threshold of detection and the recorded pixel intensity is then truncated at the threshold. Truncation of the pixel intensity causes the estimates of gene expression (i.e., intensity) to be biased. Microarray experiments are commonly affected by saturated pixels; as a result all higher level analyses are made on these biased gene expression estimates. In this paper, we propose a method for improving the quality of the signal for cDNA microarrays by making use of several scans at varying scanner sensitivities. For each spot, pixel level intensity readings are given as input to a Bayesian hierarchical model. The model uses the pixel intensities of the spot to provide a posterior distribution of the true expression level of the corresponding genes. The parameters of the hierarchical model are estimated jointly with these expression levels, thus performing an integrated analysis of the measurement data. The method improves in all ranges the accuracy with which intensities can be estimated and extends the dynamic range of measured gene expression at the high end. The method is generic and can be applied to data from any organism and for imaging with any scanner. Results from a real data set illustrate an improved precision in the estimation of the expression of genes compared to what can be achieved by applying standard methods and using only a single scan.

Bayes Theorem↗

PubMed1990

Determination of physiological levels of glucose in an aqueous matrix with digitally filtered Fourier transform near-infrared spectra.

A procedure is described for the measurement of clinically relevant concentrations of glucose in aqueous solutions with near-infrared (NIR) absorbance spectroscopy. A glucose band centered at 4400 cm-1 is used for this analysis. NIR spectra are collected over the frequency range 5000-4000 cm-1 with a Fourier transform spectrometer. A narrow-band-pass optical interference filter is placed in the optical path of the spectrometer to eliminate light outside this restricted range. This configuration provides a 2.9-fold reduction in spectral noise by utilizing the dynamic range of the detector solely for light transmitted through the filter. In addition, a novel spectral processing scheme is described for extracting glucose concentration information from the resulting absorbance spectra. The key component of this scheme is a digital Fourier filter that removes both high-frequency noise and low-frequency base-line variations from the spectra. Numerical optimization procedures are used to identify the best location and width of a Gaussian-shaped frequency response function for this Fourier filter. A dynamic area calculation, coupled with a simple linear base-line correction, provides an integrated area from the processed spectra that is linearly related to glucose concentrations over the range 1-20 mM. The linear calibration model accurately predicted glucose levels in a series of test solutions with an overall mean percent error of 2.5%. Based on the uncertainty in the parameters defining the calibration model and the variability of the magnitudes of the integrated areas, an overall uncertainty of 7.8% was estimated for predicted glucose concentrations.

Calibration↗

PubMedDate not supplied

Low-light imaging technology in the life sciences.

Photon imaging is an increasingly important technique for the measurement and analysis of chemiluminescence and bioluminescence. New high-performance low-light level imaging systems have recently become available for the life sciences. These systems use advances in camcera design and digital image processing and are now being used for a wide range of luminescence applications. They offer good sensitivity for photon detection and large dynamic range, and are suitable for quantitative analysis. This is achieved using a range of software techniques including image arithmetic, histogramming or summing regions of interest, feature extraction and multiple image processing for kinetics or assay screening. Improvements in image-processing hardware and software have increased the usefulness of these systems in the biosciences. Low-light imaging is a rapid and non-invasive method for the sensitive detection and analysis of luminescent assays. As such it offers a powerful and sensitive tool for investigating processes, both at the cellular level (luc and lux reporter genes, intracellular signalling) and for measurement of macro samples (immunoassays, gels and blots, tissue sections).

Animals↗

PubMed2000

Bioanalytical high-throughput selected reaction monitoring-LC/MS determination of selected estrogen receptor modulators in human plasma: 2000 samples/day.

The high-throughput determination of small molecules in biological matrixes has become an important part of drug discovery. This work shows that increased throughput LC/MS/MS techniques can be used for the analysis of selected estrogen receptor modulators in human plasma where more than 2000 samples may be analyzed in a 24-h period. The compounds used to demonstrate the high-throughput methodology include tamoxifen, raloxifene, 4-hydroxytamoxifen, nafoxidine, and idoxifene. Tamoxifen and raloxifene are used in both breast cancer therapy and osteoporosis and have shown prophylactic potential for the reduction of the risk of breast cancer. The described strategy provides LC/MS/MS separation and quantitation for each of the five test articles in control human plasma. The method includes sample preparation employing liquid-liquid extraction in the 96-well format, an LC separation of the five compounds in less than 30 s, and selected reaction monitoring detection from low nano- to microgram per milliter levels. Precision and accuracy are determined where each 96-well plate is considered a typical "tray" having calibration standards and quality control (QC) samples dispersed through each plate. A concept is introduced where 24 96-well plates analyzed in 1 day is considered a "grand tray", and the method is cross-validated with standards placed only at the beginning of the first plate and the end of the last plate. Using idoxifene-d5 as an internal standard, the results obtained for idoxifene and tamoxifen satisfy current bioanalytical method validation criteria on two separate days where 2112 and 2304 samples were run, respectively. Method validation included 24-h autosampler stability and one freeze-thaw cycle stability for the extracts. Idoxifene showed acceptable results with accuracy ranging from 0.3% for the high quality control (QC) to 15.4% for the low QC and precision of 3.6%-13.9% relative standard deviation. Tamoxifen showed accuracy ranging from 1.6% to 13.8% and precision from 7.8% to 15.2%. The linear dynamic range for these compounds was 3 orders of magnitude. The limit of quantification was 5 and 50 ng/ mL for tamoxifen and idoxifene, respectively. The other compounds in this study in general satisfy the more relaxed bioanalytical acceptance criteria for modern drug discovery. It is suggested that the quantification levels reported in this high-throughput analysis example are adequate for many drug discovery and related early pharmaceutical studies.

Chromatography, Liquid↗

PubMed1997

Influence of picrotoxin and strychnine on the spectral sensitivity of the turtle ERG b- and d-wave: I. Dark adaptation.

The ERG ON- (b-wave) and OFF-response (d-wave) to differently coloured stimuli was studied using a wide range of stimulus intensities in dark adapted turtle retina. The intensity-response curve of the b-wave showed saturation but that of the d-wave, decline in the high-intensity stimulus range. The curves of the relative spectral sensitivity of the ERG ON- and OFF-response were similar and showed a maximum in the longwave part of the spectrum. GABAergic blockade by 50 mumol L-1 picrotoxin caused an increase of the sensitivity, contrast sensitivity and the amplitude range of both ON- and OFF-responses without narrowing of the response dynamic range. In the range of lower stimulus intensities the ON-responses to blue stimuli and the OFF-responses to red stimuli were affected to a greater extent. An increased ERG b- and d-wave sensitivity was also observed during glycinergic blockade by 50 mumol L-1 strychnine. In the low intensity stimulus range the effect was maximal on the ON-response to blue stimuli and on the OFF-responses to 570 nm stimuli. It was concluded that the GABA- and glycinergic systems in the retina equalize rather than make different the relative spectral sensitivities of the ON- and OFF-responses.

Animals↗

PubMed2002

Evaluation of an improved immunoturbidimetic assay for serum C-reactive protein on a COBAS INTEGRA 400 Analyzer.

Recent studies have shown that C-reactive protein (CRP) can be used as a prognostic risk marker of cardiovascular disease. This new clinical indication requires accurate and precise measurement of CRP at low concentrations (<5 mg/L). We evaluated the analytical performance of an improved CRP immunoturbidimetric method (CRPLX from Roche Diagnostics) on a COBAS INTEGRA 400 analyzer. The assay is simple and rapid to perform with low sample volume (2.5 microl). The limit of detection is 0.26 mg/L, with a working range extending to 194 mg/l. The method shows low imprecision in the whole dynamic range, with a day-to-day coefficient of variation of 10% at a CRP concentration of 0.66 mg/L. There is no interference by bilirubin, hemoglobin, triglycerides and rheumatoid factor up to high concentrations. It compares well with a high sensitivity nephelometric assay, widely used as reference method, and with a classical turbidimetric assay. We conclude that this CRP assay offers to the clinical laboratory an efficient and reliable alternative tohigh sensitivity immunoassays in the new CRP applications.

Autoanalysis↗

PubMed1990

Speech-reception threshold in noise for hearing-impaired listeners in conditions with a varying amplitude-frequency response.

In a study on the effects of a frequency-dependent automatic gain control in hearing-aids, two experiments were carried out with hearing-impaired listeners. In the first experiment, the effect of varying the amplitude-frequency response on the speech-reception threshold (SRT) of sentences presented in noise was studied. The noise had the same spectrum as the long-term average spectrum of the sentences. Results suggest that the amplitude-frequency response may vary within a range from, roughly, -3 to +10 dB/oct relative to the bisector of the dynamic range, without giving an increase in SRT larger than 2 dB. In the second experiment, the effect on masked SRT of adjusting the amplitude-frequency response to situations of seriously interfering low-frequency noise was studied. Again, the noise had a spectrum identical with the long-term average spectrum of the sentences, but this time the noise level in one octave band was increased by 20 dB. Preliminary results indicate that a selective attenuation of the signal in the band containing the extra noise may give a decrease of masked SRT up to 4.5 dB.

Audiometry, Pure-Tone↗

PubMed1990

ERG-determined spectral and absolute sensitivities in relation to age and size in the halfcrab Petrolisthes elongatus (Crustacea; Decapoda; Anomura).

The electroretinogram (ERG) waveform of Petrolisthes elongatus is biphasic and transient and does not change with age (monitored as carapace length and weight of the individual). Though there was a very slight decrease in sensitivity with age (R2 = 0.008), spectral peaks and curves remained virtually unchanged. A shift of 2.2 log units in threshold sensitivity, however, was observed in relation to the different adaptational states. The greatest difference, not unexpectedly, occurred between dark-adapted eyes, tested at night, and light-adapted eyes tested during the day at a background illumination of 250 1x. The gradient of the V/LogI curve (n) in light-adapted animals increased, which means a smaller increase in intensity is required to produce an increase in response compared to a dark-adapted animal, but there was no difference in n with regard to the different age-groups. Also, no significant difference was noticed between dark-adapted eyes tested during day and night. It is concluded that the intensity range over which vision in P. elongatus is maximally sensitive to contrast (the dynamic range) is 2.5-3.0 log units. Since there is apparently little or no alteration in the photic environment and the behaviour of P. elongatus as it ages, there is no advantage in fundamentally altering the parameters of the absolute and spectral sensitivity function with age. Our observations suggest that the eyes are able to adjust within 30 min to changing ambient light levels irrespective of whether or not a circadian activity rhythm operates.

Age Factors↗

PubMed1986

Stimulus investigative range in the perimetry of retinitis pigmentosa: some preliminary findings.

The manipulation of perimetric stimulus parameters over a given dynamic range has been reported to provide diagnostic information additional to that of changes in differential sensitivity. Preliminary studies (Flanagan et al., 1984a) have indicated that the perimetric response in retinitis pigmentosa behaves atypically over a range of stimulus combinations and strategies. The current study investigated the perimetric response of 17 retinitis pigmentosa patients of various genetic types over a range of stimulus parameters (target size, presentation time and background luminance) and test strategies (kinetic and threshold static) using the Octopus automated perimeter, the Goldmann and Tubinger bowl perimeters and the Dicon Autoperimeter 3000. Statokinetic dissociation was found to be present with large target sizes at 10 asb and 31.5 asb bowl luminances. Some patients demonstrated enhanced sensitivity to shorter stimulus presentations.

Adult↗

PubMed2003

Attomole sensitivity for unlabeled proteins and polypeptides with on-chip capillary electrophoresis and universal detection by interferometric backscatter.

A universal detector based on backscatter interferometry has been developed to perform nanoliter volume refractive index measurements for on-chip sodium dodecyl sulfate (SDS) gel based (polyethylene oxide gel) separations and quantification label-free proteins. The on-chip interferometric backscatter detector (OCIBD) system consists of a simple, folded optical train based on the interaction of a laser beam with an etched channel in the shape of half cylinder in a fused-silica plate. The backscattered light from the channel takes on the form of a high-contrast interference pattern that contains information related to the bulk properties of the fluid located within the probe or detection volume of 2.32 x 10(-9) L. Depending on capillary electrophoresis (CE) injection method, the positional changes of the interference pattern extrema (fringes) allow for the quantification of unlabeled proteins at levels ranging from 11 to 310 amol (2.7 x 10(-8)mol/L) with a linear dynamic range of 2.5 decades (egg albumin). Using OCIBD microchannel-based SDS capillary gel electrophoresis (SDS/CGE), separation and detection of five label-free proteins was achieved in less than 100 seconds with detection limits ranging from 0.95 pg (1.1 x 10(-16)mol or 2.5 x 10(-7)mol/L) of calmodulin to 7.0 pg (1.0 x 10(-16)mol or 2.4 x 10(-7)mol/L) for bovine serum albumin (BSA) without signal filtering or active thermal control. This development shows that a universal detector based on backscatter interferometry can be used effectively for on-chip label-free solute analysis.

Animals↗

PubMed2001

Design and performance of an ESI interface for selective external ion accumulation coupled to a Fourier transform ion cyclotron mass spectrometer.

The coupling of Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) with electrospray ionization has advanced the analysis of large biopolymers and provided the basis for high-throughput protein characterization (e.g., for rapid "proteome" analyses). In this work, the combination of high-performance capillary liquid chromatography with FTICR mass spectrometry and external ion accumulation has been shown to increase both sensitivity and analysis duty cycle. Instrument versatility is further improved by ion preselection followed by ion accumulation in an external linear quadrupole ion trap. The interface was tested with a 3.5-T FTICR mass spectrometer and evaluated with a number of peptides and proteins whose molecular weights ranged from 500 to 66000. A significant increase in the sensitivity, duty cycle, and dynamic range over that of the previously used accumulated trapping was achieved, exhibiting a detection limit of approximately 10 zmol (approximately 6000 molecules) for smaller proteins such as cytochrome c. Capillary LC external accumulation interface with FTICR was successfully applied for the study of whole-proteome mouse tryptic digests.

Animals↗

PubMed2005

Determination of biochemical species on electrophoresis chips with an external contactless conductivity detector.

Contactless conductivity measurements were found to be suitable for the direct detection, i.e., without needing any labels, of a range of biochemically relevant species, namely amino acids, peptides, proteins, immunoglobulin, and DNA. It was also possible to monitor the products of the enzymatic digestion of HSA with pepsin. Detection was carried out on bare electrophoresis chips made from poly(methyl methacrylate) by probing the conductivity in the channel with a pair of external electrodes, which are fixed on the chip holder. Separation efficiencies up to 15,000 plates could be obtained and LODs are in the low muM-range, except for immunoglobulin G (IgG) which could be determined down to 0.4 nM. Linear dynamic ranges of two to three orders of magnitude were obtained for the peptides as examples.

Amino Acids↗