The structure and precision of retinal spike trains

Assessing the reliability of neuronal spike trains is fundamental to an understanding of the neural code. We measured the reproducibility of retinal responses to repeated visual stimuli. In both tiger salamander and rabbit, the retinal ganglion cells responded to random flicker with discrete, brief periods of firing. For any given cell, these firing events covered only a small fraction of the total stimulus time, often less than 5%. Firing events were very reproducible from trial to trial: the timing jitter of individual spikes was as low as 1 msec, and the standard deviation in spike count was often less than 0.5 spikes. Comparing the precision of spike timing to that of the spike count showed that the timing of a firing event conveyed several times more visual information than its spike count. This sparseness and precision were general characteristics of ganglion cell responses, maintained over the broad ensemble of stimulus waveforms produced by random flicker, and over a range of contrasts. Thus, the responses of retinal ganglion cells are not properly described by a firing probability that varies continuously with the stimulus. Instead, these neurons elicit discrete firing events that may be the fundamental coding symbols in retinal spike trains.

Effects of unique ion chemistry on thin-film growth by plasma–surface interactions

Plasma processing is a standard industrial method for the modification of material surfaces and the deposition of thin films. Polyatomic ions and neutrals larger than a triatomic play a critical role in plasma-induced surface chemistry, especially in the deposition of polymeric films from fluorocarbon plasmas. In this paper, low energy CF3+ and C3F5+ ions are used to modify a polystyrene surface. Experimental and computational studies are combined to quantify the effect of the unique chemistry and structure of the incident ions on the result of ion-polymer collisions. C3F5+ ions are more effective at growing films than CF3+, both at similar energy/atom of ≈6 eV/atom and similar total kinetic energies of 25 and 50 eV. The composition of the films grown experimentally also varies with both the structure and kinetic energy of the incident ion. Both C3F5+ and CF3+ should be thought of as covalently bound polyatomic precursors or fragments that can react and become incorporated within the polystyrene surface, rather than merely donating F atoms. The size and structure of the ions affect polymer film formation via differing chemical structure, reactivity, sticking probabilities, and energy transfer to the surface. The different reactivity of these two ions with the polymer surface supports the argument that larger species contribute to the deposition of polymeric films from fluorocarbon plasmas. These results indicate that complete understanding and accurate computer modeling of plasma–surface modification requires accurate measurement of the identities, number densities, and kinetic energies of higher mass ions and energetic neutrals.

Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells

Fluorescein-labeled oligodeoxynucleotides (oligos) were introduced into cultured rat myoblasts, and their molecular movements inside the nucleus were studied by fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). FCS revealed that a large fraction of both intranuclear oligo(dT) (43%) and oligo(dA) (77%) moves rapidly with a diffusion coefficient of 4 × 10−7 cm2/s. Interestingly, this rate of intranuclear oligo movement is similar to their diffusion rates measured in aqueous solution. In addition, we detected a large fraction (45%) of the intranuclear oligo(dT), but not oligo(dA), diffusing at slower rates (≤1 × 10−7 cm2/s). The amount of this slower-moving oligo(dT) was greatly reduced if the oligo(dT) was prehybridized in solution with (unlabeled) oligo(dA) prior to introduction to cells, presumably because the oligo(dT) was then unavailable for subsequent hybridization to endogenous poly(A) RNA. The FCS-measured diffusion rate for much of the slower oligo(dT) population approximated the diffusion rate in aqueous solution of oligo(dT) hybridized to a large polyadenylated RNA (1.0 × 10−7 cm2/s). Moreover, this intranuclear movement rate falls within the range of calculated diffusion rates for an average-sized heterogeneous nuclear ribonucleoprotein particle in aqueous solution. A subfraction of oligo(dT) (15%) moved over 10-fold more slowly, suggesting it was bound to very large macromolecular complexes. Average diffusion coefficients obtained from FRAP experiments were in agreement with the FCS data. These results demonstrate that oligos can move about within the nucleus at rates comparable to those in aqueous solution and further suggest that this is true for large ribonucleoprotein complexes as well.

Parallel detection of violations of color constancy

The perceived colors of reflecting surfaces generally remain stable despite changes in the spectrum of the illuminating light. This color constancy can be measured operationally by asking observers to distinguish illuminant changes on a scene from changes in the reflecting properties of the surfaces comprising it. It is shown here that during fast illuminant changes, simultaneous changes in spectral reflectance of one or more surfaces in an array of other surfaces can be readily detected almost independent of the numbers of surfaces, suggesting a preattentive, spatially parallel process. This process, which is perfect over a spatial window delimited by the anatomical fovea, may form an early input to a multistage analysis of surface color, providing the visual system with information about a rapidly changing world in advance of the generation of a more elaborate and stable perceptual representation.

Simultaneous assessment of loss of heterozygosity at multiple microsatellite loci using semi-automated fluorescence-based detection: subregional mapping of chromosome 4 in cervical carcinoma.

Detection of loss of heterozygosity (LOH) by comparison of normal and tumor genotypes using PCR-based microsatellite loci provides considerable advantages over traditional Southern blotting-based approaches. However, current methodologies are limited by several factors, including the numbers of loci that can be evaluated for LOH in a single experiment, the discrimination of true alleles versus "stutter bands," and the use of radionucleotides in detecting PCR products. Here we describe methods for high throughput simultaneous assessment of LOH at multiple loci in human tumors; these methods rely on the detection of amplified microsatellite loci by fluorescence-based DNA sequencing technology. Data generated by this approach are processed by several computer software programs that enable the automated linear quantitation and calculation of allelic ratios, allowing rapid ascertainment of LOH. As a test of this approach, genotypes at a series of loci on chromosome 4 were determined for 58 carcinomas of the uterine cervix. The results underscore the efficacy, sensitivity, and remarkable reproducibility of this approach to LOH detection and provide subchromosomal localization of two regions of chromosome 4 commonly altered in cervical tumors.

Negative activation enthalpies in the kinetics of protein folding.

Although the rates of chemical reactions become faster with increasing temperature, the converse may be observed with protein-folding reactions. The rate constant for folding initially increases with temperature, goes through a maximum, and then decreases. The activation enthalpy is thus highly temperature dependent because of a large change in specific heat (delta Cp). Such a delta Cp term is usually presumed to be a consequence of a large decrease in exposure of hydrophobic surfaces to water as the reaction proceeds from the denatured state to the transition state for folding: the hydrophobic side chains are surrounded by "icebergs" of water that melt with increasing temperature, thus making a large contribution to the Cp of the denatured state and a smaller one to the more compact transition state. The rate could also be affected by temperature-induced changes in the conformational population of the ground state: the heat required for the progressive melting of residual structure in the denatured state will contribute to delta Cp. By examining two proteins with different refolding mechanisms, we are able to find both of these two processes; barley chymotrypsin inhibitor 2, which refolds from a highly unfolded state, fits well to a hydrophobic interaction model with a constant delta Cp of activation, whereas barnase, which refolds from a more structured denatured state, deviates from this ideal behavior.

In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries.

A method for isolating and cloning mRNA populations from individual cells in living, intact plant tissues is described. The contents of individual cells were aspirated into micropipette tips filled with RNA extraction buffer. The mRNA from these cells was purified by binding to oligo(dT)-linked magnetic beads and amplified on the beads using reverse transcription and PCR. The cell-specific nature of the isolated mRNA was verified by creating cDNA libraries from individual tomato leaf epidermal and guard cell mRNA preparations. In testing the reproducibility of the method, we discovered an inherent limitation of PCR amplification from small amounts of any complex template. This phenomenon, which we have termed the "Monte Carlo" effect, is created by small and random differences in amplification efficiency between individual templates in an amplifying cDNA population. The Monte Carlo effect is dependent upon template concentration: the lower the abundance of any template, the less likely its true abundance will be reflected in the amplified library. Quantitative assessment of the Monte Carlo effect revealed that only rare mRNAs (< or = 0.04% of polyadenylylated mRNA) exhibited significant variation in amplification at the single-cell level. The cDNA cloning approach we describe should be useful for a broad range of cell-specific biological applications.

Vapor-liquid equilibria using the Gibbs energy and the common tangent plane criterion

Phase thermodynamics is often perceived as a difficult subject that many students never become fully comfortable with. The Gibbsian geometrical framework can help students to gain a better understanding of phase equilibria. An exercise to interpret the vapor-liquid equilibrium of a binary azeotropic mixture, using the equilibrium condition based on the common tangent plane criterion (the Gibbs stability test), is presented in this paper. From a T-composition phase diagram for the mixture, the temperature is set at different values: above, intermediate to, and below the boiling temperatures of the pure components, to intersect different regions of the system. Students prepare an Excel spreadsheet where the Gibbs energy of mixing of the vapor and liquid mixtures are calculated and represented over the whole range of compositions and then, apply the Gibbs stability test to ascertain the aggregation state of the system and to calculate the VL phase equilibrium compositions. Finally, Matlab is used to generate the 3D Gibbs energy of mixing surfaces for both phases over the whole range of temperatures which facilitates the geometrical interpretation of the vapor-liquid equilibrium.

Color representation and interpretation of special effect coatings

A representation of the color gamut of special effect coatings is proposed and shown for six different samples, whose colors were calculated from spectral bidirectional reflectance distribution function (BRDF) measurements at different geometries. The most important characteristic of the proposed representation is that it allows a straightforward understanding of the color shift to be done both in terms of conventional irradiation and viewing angles and in terms of flake-based parameters. A different line was proposed to assess the color shift of special effect coatings on a*,b*-diagrams: the absorption line. Similar to interference and aspecular lines (constant aspecular and irradiation angles, respectively), an absorption line is the locus of calculated color coordinates from measurement geometries with a fixed bistatic angle. The advantages of using the absorption lines to characterize the contributions to the spectral BRDF of the scattering at the absorption pigments and the reflection at interference pigments for different geometries are shown.

Benthic foraminifera of late Quaternary sediments in the northern North Atlantic

Four long sediment cores from locations in the Framstrait, the Norwegian-Greenland Seas and the northern North Atlantic were analysed in a high resolution sampling mode (1 - 2 cm density) for their benthic foraminiferal content. In particular the impact of the intense climatic changes at glacial/interglacial transitions (terminations I and II) on the benthic community have been of special interest. The faunal data were investigated by means of multivariate analysis and represented in their chronological occurence. The most prominent species of benthic foraminifera in the Norwegian-Greenland Seas are Oridorsalis umbonatus, Cibicidoides wuellerstorfi, the group of Cassidulina, Pyrgo rotalaria, Globocassidulina subglobosa and fragmented tubes of arenaceous species. The climatic signal of termination I as well as termination II is recorded in the fossil foraminiferal tests as divided transition from glacial to interglacial. The elder INDAR maximum (individuals accumulation rate = individuals/sq cm * 1.000 y; Norwegian-Greenland Seas: average 3.000 - 6.000 individuals/sq cm * 1.000 y; northern North Atlantic: average 150 individuals/sq cm * 1.000 y) is followed by a period of decreased values. The second, younger maximum reaches comparable values as the elder maximum. The interglacial INDAR are in average 700 individuals/sq cm * 1.000 y in the Norwegian-Greenland Seas and 200 individuals/sq cm * 1.000 y in average in the northern North Atlantic. The occurence of the elder INDAR maximum shows a distinct chronological transgressivity between the northern North Atlantic (12.400 ybp.) and the Framstrait (8.900 ybp.). The time shift from south to north amounts 3.500 yrs., the average expanding velocity 0,78 km per year. Within the Norwegian-Greenland Seas the average expanding velocity amounts 0,48 km per year. This chronological transgressivity is interpreted as impact of the progressive expanding of the North Atlantic and the Norwegian Current during the deglaciation. The dynamic of the faunal development is defined as increasing INDAR per time. The elder INDAR maximum shows in both glacial/interglacial transitions an exponential increase from south to north. Termination II is characterized by a general higher dynamic as termination I. By means of the high resolution sampling density the impact of regional isotopic recognized melt-water events is recognized by an increase of endobenthic and t-ubiquitous species in the Norwegian-Greenland Seas sediments. During termination I the relative minimum between both INDAR maxima occur chronological with an decrease of calculated sea surface temperatures. This is interpreted as indication of the close pelagic - benthic coupling. The climatic signal in the northern North Atlantic recorded in the fossil benthic foraminiferal community shows a lower amplitude as in the Norwegian-Greenland Seas. The occurence of the epibenthic Cibicidoides wuellersforfi allows to evaluate the variability of the bottom water mass. In general at all core locations increasing lateral bottom currents are recognized with the occurence of the second younger INDAR maximum. In comparison with various paleo-climatological data sets fossil benthic foraminifers show a distinct koherence with changes of the atmospheric temperatures, the SSTs and the postglacial sea level increase. The benthic foraminiferal fauna is bound indirectly on and indicative for regional climatic changes, but principal dependent upon global climatic changes.

(Table 1) Some structural characteristics of communities and detritus flux through the lower boundary of a given water column in different regions of the Kara Sea

Vertical fluxes of autochtonous detritus at different levels were estimated using the algorithm of structure-function analysis. The calculations are based on pelagic ecosystem parameters in the Kara Sea observed in September 1993 (temperature, primary production, biomass of phytoplankton, bacteria, protozoa, and zooplankton, trophic and size composition, etc.). At eight stations in different parts of the sea where sedimentation traps were set, the range of calculated fluxes of autochtonous detritus through the lower boundary of the water column was 13-90 mgC/m**2/day. The flux was much higher in the estuary of the Yenisey River (55-90 mgC/m**2/day) than in the northeastern regions (I8-50 mgC/m**2/day) and, especially, in the relatively deep southwestern part of the sea (13-35 mgC/m**2/day). The calculated fluxes of autochtonous detritus in shallow water regions (where conditions are variable and poorly known hydrologically and where outflow of allochtonous detritus is substantial) cannot be compared to data from sedimentation traps.

Evaluation of individual protein errors in silver-stained two-dimensional gels

The relationship between spot volume and variation for all protein spots observed on large format 2D gels when utilising silver stain technology and a model system based on mammalian NSO cell extracts is reported. By running multiple gels we have shown that the reproducibility of data generated in this way is dependent on individual protein spot volumes, which in turn are directly correlated with the coefficient of variation. The coefficients of variation across all observed protein spots were highest for low abundant proteins which are the primary contributors to process error, and lowest for more abundant proteins. Using the relationship between spot volume and coefficient of variation we show it is necessary to calculate variation for individual protein spot volumes. The inherent limitations of silver staining therefore mean that errors in individual protein spot volumes must be considered when assessing significant changes in protein spot volume and not global error. (C) 2003 Elsevier Science (USA). All rights reserved.

Bubble load measurement in the pulp zone of industrial flotation machines - a new device for determining the froth recovery of attached particles

A new device has been developed to directly measure the bubble loading of particle-bubble aggregates in industrial flotation machines, both mechanical flotation cells as well as flotation column cells. The bubble loading of aggregates allows for in-depth analysis of the operating performance of a flotation machine in terms of both pulp/collection zone and froth zone performance. This paper presents the methodology along with an example showing the excellent reproducibility of the device and an analysis of different operating conditions of the device itself. (C) 2004 Elsevier B.V All rights reserved.

Effect of inspiratory flow on methacholine challenge in children

Regulation of inspiratory flow alters the outcomes of the methacholine (MHC) challenge in adults and cough receptor sensitivity in children. The effect of inspiratory flow on the reproducibility of the MHC challenge in children is unknown. The aim of this study was to evaluate the effect of inspiratory flow alteration on the repeatabilty of the MHC challenge in children with and without asthma. Twenty-five children undertook the MHC challenge on three different days by using a dosimeter connected to a setup that allowed regulation of inspiratory flow and pattern. Children were randomized to commence the challenges at 20 or 60 L/min, and the last challenge was performed at 20 L/min. The within-subject standard deviation, 95% range for change, and doubling dose for the differing inspiratory flow (20 vs. 60 L/min) was more than twice that of when inspiratory flow was maintained at 20 L/min for both occasions. The range of the limits of agreement of the Bland and Altman plot was smaller when inspiratory flow was constant. For short-term comparative individual studies in children, inspiratory flow should be regulated. Laboratories and research measuring change in airway hyperrepsonsiveness to MHC should determine and report reproducibility indices of the challenge so airway hyperresponsiveness changes can be interpreted meaningfully.

Reconsidering the use of photosynthetic bacteria for removal of sulfide from wastewater

The feasibility of using photosynthetic sulfide-oxidizing bacteria to remove sulfide from wastewater in circumstances where axenic cultures are unrealistic has been completely reconsidered on the basis of known ecophysiological data, and the principles of photobioreactor and chemical reactor engineering. This has given rise to the development of two similar treatment concepts relying on biofilms dominated by green sulfur bacteria (GSB) that develop on the exterior of transparent surfaces suspended in the wastewater. The GSB are sustained and selected for by radiant energy in the band 720 - 780 nm, supplied from within the transparent surface. A model of one of these concepts was constructed and with it the reactor concept was proven. The dependence of sulfide-removal rate on bulk sulfide concentration has been ascertained. The maximum net areal sulfide removal rate was 2.23 g m(-2) day(-1) at a bulk sulfide concentration of 16.5 mg L-1 and an incident irradiance of 1.51 W m(-2). The system has a demonstrated capacity to mitigate surges in sulfide load, and appears to use much less radiant power than comparable systems. The efficacy with which this energy was used for sulfide removal was 1.47 g day(-1) W-1. The biofilm was dominated by GSB, and evidence gathered indicated that other types of phototrophs were not present. (C) 2004 Wiley Periodicals, Inc.