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PubMed2006

A stimulus-dependent dissociation between the cerebral hemispheres under free-viewing conditions.

Under free-viewing conditions, the leftward stimulus features are frequently overestimated (pseudoneglect). This asymmetry could reflect the operation of: (a) spatial attention mechanisms in the right hemisphere (RH) or, (b) stimulus-specific activation. To test these propositions, we attempted to induce a stimulus-specific dissociation between the hemispheres under free-viewing conditions. In two experiments (n=23, n=22) dextrals carried out two tasks. The 'grayscales' task required luminance judgments between two mirror-reversed luminance gradients. The flicker task required temporal frequency judgments between two mirror-reversed temporal gradients. The grayscales and flicker tasks suited the processing styles of the right and left hemispheres, respectively. For both experiments, a strong leftward bias was observed for the grayscales task, which could be the result of both of the mechanisms outlined above. In Experiment 1, there was a rightward bias for the flicker task-but only for participants with longer reaction times. In Experiment 2, where all responses were delayed, a rightward bias was found for the flicker task for shorter stimuli. The data demonstrate that stimulus-specific dissociations can be induced under free-viewing conditions. However, the fact that the rightward bias was: (a) weaker than the leftward bias and, (b) reduced by increases in length, demonstrates that RH spatial attention mechanisms are also important.

Adolescent↗
PubMed2005

GATA: a graphic alignment tool for comparative sequence analysis.

BACKGROUND: Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dot plot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments. RESULTS: To address some of these issues, we created a stand alone, platform independent, graphic alignment tool for comparative sequence analysis (GATA http://gata.sourceforge.net/). GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF) file. CONCLUSIONS: GATA uses the NCBI-BLASTN program in conjunction with post-processing to exhaustively align two DNA sequences. It provides researchers with a fine-grained alignment and visualization tool aptly suited for non-coding, 0-200 kb, pairwise, sequence analysis. It functions independent of sequence feature ordering or orientation, and readily visualizes both large and small sequence inversions, duplications, and segment shuffling. Since the alignment is visual and does not contain gaps, gene annotation can be added to both sequences to create a thoroughly descriptive picture of DNA conservation that is well suited for comparative sequence analysis.

Algorithms↗
PubMed2004

Defined types of cortical interneurone structure space and spike timing in the hippocampus.

The cerebral cortex encodes, stores and combines information about the internal and external environment in rhythmic activity of multiple frequency ranges. Neurones of the cortex can be defined, recognized and compared on the comprehensive application of the following measures: (i) brain area- and cell domain-specific distribution of input and output synapses, (ii) expression of molecules involved in cell signalling, (iii) membrane and synaptic properties reflecting the expression of membrane proteins, (iv) temporal structure of firing in vivo, resulting from (i)-(iii). Spatial and temporal measures of neurones in the network reflect an indivisible unity of evolutionary design, i.e. neurones do not have separate structure or function. The blueprint of this design is most easily accessible in the CA1 area of the hippocampus, where a relatively uniform population of pyramidal cells and their inputs follow an instantly recognizable laminated pattern and act within stereotyped network activity patterns. Reviewing the cell types and their spatio-temporal interactions, we suggest that CA1 pyramidal cells are supported by at least 16 distinct types of GABAergic neurone. During a given behaviour-contingent network oscillation, interneurones of a given type exhibit similar firing patterns. During different network oscillations representing two distinct brain states, interneurones of the same class show different firing patterns modulating their postsynaptic target-domain in a brain-state-dependent manner. These results suggest roles for specific interneurone types in structuring the activity of pyramidal cells via their respective target domains, and accurately timing and synchronizing pyramidal cell discharge, rather than providing generalized inhibition. Finally, interneurones belonging to different classes may fire preferentially at distinct time points during a given oscillation. As different interneurones innervate distinct domains of the pyramidal cells, the different compartments will receive GABAergic input differentiated in time. Such a dynamic, spatio-temporal, GABAergic control, which evolves distinct patterns during different brain states, is ideally suited to regulating the input integration of individual pyramidal cells contributing to the formation of cell assemblies and representations in the hippocampus and, probably, throughout the cerebral cortex.

Animals↗
PubMed2000

Two-photon fluorescence microscopy studies of bipolar tetraether giant liposomes from thermoacidophilic archaebacteria Sulfolobus acidocaldarius.

The effects of temperature and pH on Laurdan (6-lauroyl-2-(dimethylamino)naphthalene) fluorescence intensity images of giant unilamellar vesicles (GUVs) ( approximately 20-150 microm in diameter) composed of the polar lipid fraction E (PLFE) from the thermoacidophilic archaebacteria Sulfolobus acidocaldarius have been studied using two-photon excitation. PLFE GUVs made by the electroformation method were stable and well suited for microscopy studies. The generalized polarization (GP) of Laurdan fluorescence in the center cross section of the vesicles has been determined as a function of temperature at pH 7.23 and pH 2.68. At all of the temperatures and pHs examined, the GP values are low (below or close to 0), and the GP histograms show a broad distribution width (> 0.3). When excited with light polarized in the y direction, Laurdan fluorescence in the center cross section of the PLFE GUVs exhibits a photoselection effect showing much higher intensities in the x direction of the vesicles, a result opposite that previously obtained on monopolar diester phospholipids. This result indicates that the chromophore of Laurdan in PLFE GUVs is aligned parallel to the membrane surface. The x direction photoselection effect and the low GP values lead us to further propose that the Laurdan chromophore resides in the polar headgroup region of the PLFE liposomes, while the lauroyl tail inserts into the hydrocarbon core of the membrane. This unusual L-shaped disposition is presumably caused by the unique lipid structures and by the rigid and tight membrane packing in PLFE liposomes. The GP exhibited, at both pH values, a small but abrupt decrease near 50 degrees C, suggesting a conformational change in the polar headgroups of PLFE. This transition temperature fully agrees with the d-spacing data recently measured by small-angle x-ray diffraction and with the pyrene-labeled phosphatidylcholine and perylene fluorescence data previously obtained from PLFE multilamellar vesicles. Interestingly, the two-photon Laurdan fluorescence images showed snowflake-like lipid domains in PLFE GUVs at pH 7.23 and low temperatures (<20 degrees C in the cooling scan and <24 degrees C in the heating scan). These domains, attributable to lipid lateral separation, were stable and laterally immobile at low temperatures (<23 degrees C), again suggesting tight membrane packing in the PLFE GUVs.

2-Naphthylamine↗
PubMed2003

Theoretical simulation of tumour oxygenation and results from acute and chronic hypoxia.

The tumour microenvironment is considered to be responsible for the outcome of cancer treatment and therefore it is extremely important to characterize and quantify it. Unfortunately, most of the experimental techniques available now are invasive and generally it is not known how this influences the results. Non-invasive methods on the other hand have a geometrical resolution that is not always suited for the modelling of the tumour response. Theoretical simulation of the microenvironment may be an alternative method that can provide quantitative data for accurately describing tumour tissues. This paper presents a computerized model that allows the simulation of the tumour oxygenation. The model simulates numerically the fundamental physical processes of oxygen diffusion and consumption in a two-dimensional geometry in order to study the influence of the different parameters describing the tissue geometry. The paper also presents a novel method to simulate the effects of diffusion-limited (chronic) hypoxia and perfusion-limited (acute) hypoxia. The results show that all the parameters describing tissue vasculature are important for describing tissue oxygenation. Assuming that vascular structure is described by a distribution of inter-vessel distances, both the average and the width of the distribution are needed in order to fully characterize the tissue oxygenation. Incomplete data, such as distributions measured in a non-representative region of the tissue, may not give relevant tissue oxygenation. Theoretical modelling of tumour oxygenation also allows the separation between acutely and chronically hypoxic cells, a distinction that cannot always be seen with other methods. It was observed that the fraction of acutely hypoxic cells depends not only on the fraction of collapsed blood vessels at any particular moment, but also on the distribution of vessels in space as well. All these suggest that theoretical modelling of tissue oxygenation starting from the basic principles is a robust method that can be used to quantify the tissue oxygenation and to provide input parameters for other simulations.

Acute Disease↗
PubMed2001

A high-resolution phantom for MRI.

Assessment of spatial resolution is an important step to test the performance of new sequence techniques-especially ultrafast techniques with dedicated k-space trajectories or interpolation algorithms. Measurement of the modulation transfer function (MTF) is a rather difficult procedure, but using suitable resolution phantoms allows a simple visual evaluation of spatial resolution. In contrast to commonly used test objects with a very restricted number of resolution patterns we developed a phantom containing resolution patterns from 0.1 to 1.5 mm in steps of 0.1 mm. One resolution pattern consists of five parallel Plexiglas strips with the distance of the strips being equal to their thickness. Together with a Plexiglas cuboid the resolution patterns are mounted on a Plexiglas plate on the bottom of the cylindrical phantom. An aqueous solution of manganese chloride is used to fill the phantom. High resolution cross sections (pixel size: 50 microm) through the resolution patterns were measured to confirm the correct dimensions of the phantom. To verify the appropriateness of the 0.1 and 0.2 mm stacks micro-CT images with a pixel size of 25 microm were acquired additionally for both patterns. Besides visual inspection evaluation of the profile function of signal intensity across the stacks demonstrates that the resolution patterns are sufficiently correct. T(1)-weighted SE sequences with slightly different pixel sizes as well as T(1)- and T(2*)- weighted gradient echo sequences were applied to demonstrate some possible applications of this phantom. In conclusion, the proposed phantom is well suited to assess the spatial resolution qualitatively (i.e., visually) and quantitatively over a wide range in steps of 0.1 mm.

Humans↗
PubMed1991

Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution.

The three-dimensional structure of the human histocompatibility antigen HLA-A2 was determined at 3.5 A resolution by a combination of isomorphous replacement and iterative real-space averaging of two crystal forms. The monoclinic crystal form has now been refined by least-squares methods to an R-factor of 0.169 for data from 6 to 2.6 A resolution. A superposition of the structurally similar domains found in the heterodimer, alpha 1 onto alpha 2 and alpha 3 onto beta 2m, as well as the latter pair onto the ancestrally related immunoglobulin constant domain, reveals that differences are mainly in the turn regions. Structural features of the alpha 1 and alpha 2 domains, such as conserved salt-bridges that contribute to stability, specific loops that form contacts with other domains, and the antigen-binding groove formed from two adjacent helical regions on top of an eight-stranded beta-sheet, are analyzed. The interfaces between the domains, especially those between beta 2m and the HLA heavy chain presumably involved in beta 2m exchange and heterodimer assembly, are described in detail. A detailed examination of the binding groove confirms that the solvent-accessible amino acid side-chains that are most polymorphic in mouse and human alleles fill up the central and widest portion of the binding groove, while conserved side-chains are clustered at the narrower ends of the groove. Six pockets or sub-sites in the antigen-binding groove, of diverse shape and composition, appear suited for binding side-chains from antigenic peptides. Three pockets contain predominantly non-polar atoms; but others, especially those at the extreme ends of the groove, have clusters of polar atoms in close proximity to the "extra" electron density in the binding site. A possible role for beta 2m in stabilizing permissible peptide complexes during folding and assembly is presented.

Amino Acid Sequence↗
PubMed2000

A stereological method for testing whether or not there is random deposition of perivillous fibrin-type fibrinoid at the villous surface: description and pilot applications to term placentae.

We present a stereological method for testing whether or not there is random deposition of fibrin-type fibrinoid (FTF) at the villous surface of human placenta. The method requires random sampling of tissue with test lattice lines superimposed on microscopic fields at random positions and orientations. Test lines are used to generate chance intersections with specified sub-domains of the villous surface. At least three sub-domains are distinguishable: non-syncytial knots (nonSK), syncytial knots (SK) and areas of trophoblast de-epithelialization (DEP). Other sub-domains may be included to suit individual circumstances and project aims. The relative numbers of intersections with sub-domains provide the basis for an 'expected' distribution. Subsequently, this is compared with an 'observed' distribution which can be calculated from empirical estimates of the numbers of intersections with sub-domains associated with perivillous FTF (e.g. nonSK+FTF, SK+FTF and DEP+FTF). Expected and observed distributions can be compared by a chi-squared analysis. If the null hypothesis (no difference) is rejected, chi-squared values for individual sub-domains can be analysed in order to localize and interpret sites of preferential deposition. Comparisons may be drawn for individual placentae as well as a group of placentae, thereby permitting assessment of inter-placental variability. Finally, between-group comparisons may be drawn in order to test whether or not FTF deposition patterns differ in control and other pregnancies. Worked examples of the statistical procedures are provided. Preliminary results of applications to placentae from normal and complicated (hypobaric hypoxia) pregnancies are presented. They show that FTF deposition is non-random and preferentially located at sites of de-epithelialization. De-epithelialization may be a consequence of syncytial degeneration but also, at least in part, of continuous trophoblast turnover in which syncytial fragments rich in (pre-) apoptotic nuclei detach from the epithelium and are deported from the maternal intervillous space. The nascent detachment site is immediately covered by FTF prior to repair by re-epithelialization.

Altitude↗
PubMed2006

Spin-spin contributions to the zero-field splitting tensor in organic triplets, carbenes and biradicals-a density functional and ab initio study.

An evaluation study for the direct dipolar electron spin-spin (SS) contribution to the zero-field splitting (ZFS) tensor in electron paramagnetic resonance (EPR) spectroscopy is presented. Calculations were performed on a wide variety of organic systems where the SS contribution to the ZFS dominates over the second-order spin-orbit coupling (SOC) contribution. Calculations were performed using (hybrid) density functional theory (DFT), as well as complete active space self-consistent field (CASSCF) wave functions. In the former case, our implementation is an approximation, because we use the two-particle reduced spin-density matrix of the noninteracting reference system. In the latter case, the SS contribution is approximated by a mean-field method which, nevertheless, gives accurate results, compared to the approximation free computation of the SS part in a CASSCF framework. For the case of the triplet dioxygen molecule, it was shown that restricted open-shell density functional theory (RODFT), as well as CASSCF, can provide accurate spin-spin couplings while spin-unrestricted DFT leads to much larger errors. Furthermore, 15 organic radicals, including several 1,3 and 1,5 diradicals, dinitroxide biradicals, and even a chlorophyll a model system, were examined as test cases to demonstrate the accuracy and efficiency of our approach within a DFT framework. Accurate D values with root-mean-square deviations of 0.0035 cm(-1) were obtained. Furthermore, all trends, including those due to substituent effects, were correctly reproduced. In a different set of calculations, the polyacenes benzene, naphthalene, anthracene, and tetracene were studied. Applying DFT, the absolute D values were noticeably underestimated, but it was possible to correctly reproduce the trend to smaller D values with larger size of the systems. Finally, it was demonstrated that our approach is also well-suited for the study of carbenes. The smaller organic radicals of this work were also studied, through the use of CASSCF wave functions. This was a special advantage in the case of the triplet polyacenes, where the CASSCF approach gave better results than the DFT method. In comparing spin-restricted and spin-unrestricted results, it was shown through a natural orbital analysis and comparison to high-level ab initio calculations that even small amounts of spin polarization introduced by the unrestricted calculations lead to large deviations between the unrestricted Kohn-Sham (UKS) and restricted open-shell Kohn-Sham (ROKS) approaches. It is challenging to understand why the ROKS results show much better correlation with the experimental data.

Algorithms↗
PubMed2003

Design and application of basic amino acids displaying enhanced hydrophobicity.

Three noncoding basic amino acids, mono-, di-, and trimethyldiaminopropionic acid (mmdap, dmdap, and tmdap), have been synthesized for use in protein design. Covalent modification of a diaminopropionic acid (dap) side chain with an increasing number of methyl moieties results in a family of residues displaying short basic side chains with varying degrees of enhanced hydrophobic character. These residues may be used to introduce charged/polar interactions into the confining hydrophobic interior or interfacial spaces of proteins. As a demonstration of their utility, the ability of these residues to promote interior salt bridge formation at the helix/helix interface of GCN4-p1, a dimeric two-stranded coiled coil, was assessed. Heterodimerization mediated by buried salt bridge formation between a GCN4-based peptide containing either mmdap, dmdap, or tmdap at position 16 and an analogous peptide containing aspartic acid at the same position was studied. Mmdap-derived heterodimers are 0.5 kcal/mol more stable than the corresponding dap-derived heterodimers. This result indicates that the addition of one methyl group to the dap side chain can stabilize the heterodimeric fold. The stabilization can most likely be attributed to a decrease in the desolvation penalty incurred upon folding as well as enhanced van der Waals contacts in the folded state. The addition of three methyl groups to the dap side chain results in heterodimers that are significantly less stable than the corresponding dap-derived heterodimers, suggesting that increased steric bulk is not well accommodated in the interior of this protein. Unexpectedly, the addition of two methyl groups leads to homotrimerization of the dmdap-peptide. The resulting trimer is relatively stable (DeltaG(37)( degrees )(C) degrees = 11.8 kcal/mol) and undergoes cooperative thermal unfolding. The GCN4-p1 system exemplifies how small incremental changes in size and hydrophobicity can alter the folding preferences of a protein. Generally, this versatile suite of residues can be utilized in any protein and offer new options to the protein chemist.

Amino Acid Sequence↗
PubMedDate not supplied

Surveying patients as a start to quality improvement in the surgical suites holding area.

The holding area, as the patient's first introduction to the surgical suites, has the potential to set the tone for the entire surgical experience. To identify targets for improvement efforts in the holding area, a convenience sample of 51 surgical patients completed a 12-item patient satisfaction survey developed using Androfact before discharge from hospital. Results reveal 5 aspects that fall below the desired benchmark satisfaction rate of 80%: staff holding personal conversations in the patients' presence, being offered distraction materials while waiting, pleasantness of the physical environment, reassurance that family members would be kept up-to-date during the surgical procedure, and comfort to provide personal information without worrying that others were listening. Discussion of findings indicates priorities for improvement efforts in the holding area.

Benchmarking↗
PubMed1999

GLLS for optimally sampled continuous dynamic system modeling: theory and algorithm.

The original generalized linear least squares (GLLS) algorithm was developed for non-uniformly sampled biomedical system parameter estimation using finely sampled instantaneous measurements (D. Feng, S.C. Huang, Z. Wang, D. Ho, An unbiased parametric imaging algorithm for non-uniformly sampled biomedical system parameter estimation, IEEE Trans. Med. Imag. 15 (1996) 512-518). This algorithm is particularly useful for image-wide generation of parametric images with positron emission tomography (PET), as it is computationally efficient and statistically reliable (D. Feng, D. Ho, Chen, K., L.C. Wu, J.K. Wang, R.S. Liu, S.H. Yeh, An evaluation of the algorithms for determining local cerebral metabolic rates of glucose using positron emission tomography dynamic data, IEEE Trans. Med. Imag. 14 (1995) 697-710). However, when dynamic PET image data are sampled according to the optimal image sampling schedule (OISS) to reduce memory and storage space (X. Li, D. Feng, K. Chen, Optimal image sampling schedule: A new effective way to reduce dynamic image storage space and functional image processing time, IEEE Trans. Med. Imag. 15 (1996) 710-718), only a few temporal image frames are recorded (e.g. only four images are recorded for the four parameter fluoro-deoxy-glucose (FDG) model). These image frames are recorded in terms of accumulated radio-activity counts and as a result, the direct application of GLLS is not reliable as instantaneous measurement samples can no longer be approximated by averaging of accumulated measurements over the sampling intervals. In this paper, we extend GLLS to OISS-GLLS which deals with the fewer accumulated measurement samples obtained from OISS dynamic systems. The theory and algorithm of this new technique are formulated and studied extensively. To investigate statistical reliability and computational efficiency of OISS-GLLS, a simulation study using dynamic PET data was performed. OISS-GLLS using 4-measurement samples was compared to the non-linear least squares (NLS) method using 22-measurement samples, GLLS using 22-measurement samples and OISS-NLS using 4-measurement samples. Results demonstrated that OISS-GLLS was able to achieve parameter estimates of equivalent accuracy and reliability in comparison to NLS or GLLS using finely sampled measurements (22-measurement samples), or OISS-NLS using optimally sampled measurements (4-measurement samples). Further more, as fewer measurement samples are used in OISS-GLLS, this algorithm is computationally faster than NLS or GLLS. Therefore, OISS-GLLS is well-suited for image-wide parameter estimation when PET image data are recorded according to the optimal image sampling schedule.

Algorithms↗
PubMed2006

Correlated product distributions from ketene dissociation measured by dc sliced ion imaging.

Speed distributions of spectroscopically selected CO photoproducts of 308 nm ketene photodissociation have been measured by dc sliced ion imaging. Structured speed distributions are observed that match the clumps and gaps in the singlet CH2 rotational density of states. The effects of finite time gates in sliced ion imaging are important for the accurate treatment of quasicontinuous velocity distributions extending into the thickly sliced and fully projected regime, and an inversion algorithm has been implemented for the special case of isotropic fragmentation. With accurate velocity calibration and careful treatment of the velocity resolution, the new method allows us to characterize the coincident rotational state distribution of CH2 states as a smoothly varying deviation from an unbiased phase space theory (PST) limit, similar to a linear-surprisal analysis. High-energy rotational states of CH2 are underrepresented compared to PST in coincidence with all detected CO rotational states. There is no evidence for suppression of the fastest channels, as had been reported in two previous studies of this system by other techniques. The relative contributions of ground and first vibrationally excited singlet CH2 states in coincidence with selected rotational states of CO (upsilon=0) are well resolved and in remarkably good agreement with PST, despite large deviations from the PST rotational distributions in the CH2 fragments. At 308 nm, the singlet CH2 (upsilon2=0) and (upsilon2=1) channels are 2350 and 1000 cm(-1) above their respective thresholds. The observed vibrational branching is consistent with saturation at increasing energies of the energy-dependent suppression of rates with respect to the PST limit, attributed to a tightening variational transition state.

Journal Article↗
PubMed2006

Cell-attached voltage-clamp and current-clamp recording and stimulation techniques in brain slices.

Cell-attached recording provides a way to record the activity of - and to stimulate - neurons in brain slices without rupturing the cell membrane. This review uses theory and experimental data to address the proper application of this technique and the correct interpretation of the data. Voltage-clamp mode is best-suited for recording cell firing activity, and current-clamp mode is best-suited for recording resting membrane potential and synaptic potentials. The magnitude of the seal resistance determines what types of experiments can be accomplished with a cell-attached recording: a loose seal is adequate for recording action potential currents, and a tight seal is required for evoking action potentials in the attached cell and for recording resting and synaptic potentials. When recording action potential currents, if the researcher does not want to change the firing activity of the cell, then it is important that no current passes from the amplifier through the patch resistance. In order to accomplish this condition, the recording pipette should be held at the potential that gives a holding current of 0. An advantage of cell-attached current-clamp over whole-cell recording is that it accurately depicts whether a synaptic potential is hyperpolarizing or depolarizing without the risk of changing its polarity.

Action Potentials↗
PubMed2001

Performance of basic strategies for following gradients in two dimensions.

Computer models for following stimulus gradients in two-dimensional space were evaluated to determine the relative advantages of different strategies and to identify the issues that must be addressed in making such a comparison. The simulations were implemented with emphasis on making them as general and free of specific assumptions as possible. Performance was defined as progress along the gradient divided by the cost of the movements and time taken. Plausible values of costs were taken from data on animal energetics. The models also included various kinds of noise that limit performance. These included unintended variations and biases in motor outputs as well as sensory inputs. An initial guess at appropriate noise levels led to performance worse than that observed in experiments with leukocytes. Reduced noise levels gave good agreement. Under these, more appropriate, conditions, peak performance for the various models varied from 24 to 99% of the maximum possible. The threshold gradient required to provide performance equal to 1% of the maximum possible varied from 800 to 5000 searcher diameters per gradient decay length. Some models performed well only over a narrow range of gradients. There was no indication of a tradeoff between sensitivity to shallow gradients and high performance in steep gradients. The model of tropotaxis (simultaneous, spatial comparison) with movement in any direction was superior in having the lowest threshold, the highest maximum performance, requiring the fewest parameters to fit, and performed well over the widest range of gradients. This result suggests that amoeboid cells and echinoderms might be particularly well suited to following gradients. The modeling demonstrates the need to obtain quantitative estimates for a number of parameters (relating costs and noise levels) for a more rigorous understanding of the relative advantages of these different strategies.

Animals↗
PubMed2003

Analysis of nitric oxide consumption by erythrocytes in blood vessels using a distributed multicellular model.

Multiple sets of experimental data have shown that the red blood cell (RBC) consumes nitric oxide (NO) about 600-1000-fold slower than the equivalent concentration of cell-free hemoglobin (Hb). Diffusion barriers of various sources have been suggested to explain this observation. In this work, a multicellular, spatially distributed, two-dimensional model, that describes the production, transport, and consumption of NO in blood vessels and the surrounding tissue, is developed. The model is used to assess the relative significance of NO transport barriers that reduce the rate of NO consumption in the blood. Unlike previous models of this system, the model developed here accounts explicitly for the presence of, and interactions among, a population of RBCs inside the lumen of the blood vessel and is, therefore, better suited to analyze, quantitatively, the contribution of each transport barrier as NO diffuses from its site of synthesis to the interior of the RBCs where it interacts with Hb. The model, which uses experimentally derived parameters, shows that extracellular unstirred boundary layer diffusion alone cannot account for the reduced NO consumption by RBC compared to an equivalent concentration of cell-free Hb. Since this result is reached using a two-dimensional representation of the RBCs, which overestimates the importance of the boundary layer diffusion resistance, it would be expected that in the real three-dimensional case, diffusion through the extracellular boundary layer would contribute even less to the overall mass transfer resistance. Consistent with recent experimental findings, the results of our model suggest that, under physiological conditions, transmembrane (membrane and its associated cytoskeleton layer) diffusion limitations in RBCs represent a key source of resistance for NO uptake by RBCs.

Animals↗
PubMed2006

Biexponential characterization of prostate tissue water diffusion decay curves over an extended b-factor range.

Detailed measurements of water diffusion within the prostate over an extended b-factor range were performed to assess whether the standard assumption of monoexponential signal decay is appropriate in this organ. From nine men undergoing prostate MR staging examinations at 1.5 T, a single 10-mm-thick axial slice was scanned with a line scan diffusion imaging sequence in which 14 equally spaced b factors from 5 to 3,500 s/mm(2) were sampled along three orthogonal diffusion sensitization directions in 6 min. Due to the combination of long scan time and limited volume coverage associated with the multi-b-factor, multidirectional sampling, the slice was chosen online from the available T2-weighted axial images with the specific goal of enabling the sampling of presumed noncancerous regions of interest (ROIs) within the central gland (CG) and peripheral zone (PZ). Histology from prescan biopsy (n=9) and postsurgical resection (n=4) was subsequently employed to help confirm that the ROIs sampled were noncancerous. The CG ROIs were characterized from the T2-weighted images as primarily mixtures of glandular and stromal benign prostatic hyperplasia, which is prevalent in this population. The water signal decays with b factor from all ROIs were clearly non-monoexponential and better served with bi- vs. monoexponential fits, as tested using chi(2)-based F test analyses. Fits to biexponential decay functions yielded intersubject fast diffusion component fractions in the order of 0.73+/-0.08 for both CG and PZ ROIs, fast diffusion coefficients of 2.68+/-0.39 and 2.52+/-0.38 microm(2)/ms and slow diffusion coefficients of 0.44+/-0.16 and 0.23+/-0.16 um(2)/ms for CG and PZ ROIs, respectively. The difference between the slow diffusion coefficients within CG and PZ was statistically significant as assessed with a Mann-Whitney nonparametric test (P<.05). We conclude that a monoexponential model for water diffusion decay in prostate tissue is inadequate when a large range of b factors is sampled and that biexponential analyses are better suited for characterizing prostate diffusion decay curves.

Aged↗
PubMed2001

Glucose monitoring with long-term subcutaneous microdialysis in neonates.

BACKGROUND: Microdialysis is a new approach for continuous monitoring of small molecules in the extracellular space, and hypoglycemia is a common problem in neonatal intensive care. The objective of this study was to evaluate subcutaneous microdialysis for long-term glucose monitoring in neonatal intensive care. We determined the relative recovery of the microdialysis system in vitro and in vivo, the stability of the relative recovery in vivo during long-term microdialysis, and the correlation between blood and dialysate concentrations of glucose and urea. Furthermore, we evaluated the sensitivity and specificy of subcutaneous microdialysis for the diagnosis of hypoglycemia. PATIENT AND METHODS: Thirteen infants (10 neonates) with gestational ages of 30.2 to 45.6 weeks were investigated by microdialysis of subcutaneous adipose tissue and blood sampling. Subcutaneous microdialysis was performed for a median (range) duration of 9 (4-16) days. RESULTS: The application was safe, even in extremely low birth weight infants (<1000 g) with scanty subcutaneous adipose tissue. The mean +/- standard deviation of the relative recovery in vitro was 101 +/- 3% for glucose and 100 +/- 2% for urea. Using urea as the internal standard, the mean relative recovery in vivo was 96.4 +/- 12.7% at the beginning and remained constant up to 16 days. The correlation between microdialysate and blood was significant for glucose (r = 0.88) and urea (r = 0.98). Subcutaneous microdialysis allowed the detection of asymptomatic hypoglycemias. The diagnostic sensitivity of a dialysate glucose </=2.9 mM to predict a blood glucose level </=2.8 mM was 92.3%, with 88.1% specificy. The positive predictive value with a 13.4% prevalence of a blood glucose </=2.8 mM was 54.5%, with a negative predictive value of 98.7% and an accuracy of 88.7%. CONCLUSIONS: Subcutaneous microdialysis is a safe method, well suited for long-term glucose monitoring in neonates during intensive care. Subcutaneous microdialysis can be used to reduce blood loss and painful stress resulting from diagnostic blood sampling in high-risk neonates.

Blood Glucose↗