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Mapping multiple features in the population response of visual cortex.

Stimulus features such as edge orientation, motion direction and spatial frequency are thought to be encoded in the primary visual cortex by overlapping feature maps arranged so that the location of neurons activated by a particular combination of stimulus features can be predicted from the intersections of these maps. This view is based on the use of grating stimuli, which limit the range of stimulus combinations that can be examined. We used optical imaging of intrinsic signals in ferrets to assess patterns of population activity evoked by the motion of a texture (a field of iso-oriented bars). Here we show that the same neural population can be activated by multiple combinations of orientation, length, motion axis and speed. Rather than reflecting the intersection of multiple maps, our results indicate that population activity in primary visual cortex is better described as a single map of spatiotemporal energy.

Animals↗

Integrated network pharmacology, molecular docking and experimental validation to investigate the mechanism of tannic acid in nasopharyngeal cancer.

Tannic acid (TA) is the primary bioactive component in the gallnut (Galla chinensis) and has exhibited the anticancer effects. However, the mechanism of its anti-cancer activity in nasopharyngeal carcinoma (NPC) remains unclear. This research aims to explore the underlying mechanism of TA in the treatment of nasopharyngeal cancer using network pharmacology, molecular docking and experimental validation. Firstly, the targets of TA and NPC were predicted and collected through databases, and the intersection targets were identified. Subsequently, protein-protein interaction (PPI) network analysis, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes Genomes (KEGG) pathway enrichment analysis, molecular docking and molecular dynamics (MD) simulation were conducted to uncover the potential mechanisms of TA in treatment of NPC. Finally, in vitro experiments were utilized to verify the mechanism of TA with anticancer activity in NPC. The results of network pharmacology revealed 42 intersection targets between NPC-related targets and TA-related targets. The phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling was identified as the main target pathway of TA against NPC. Additionally, molecular docking and MD simulation confirmed the closely binding affinities of TA with AKT1. Furthermore, the results of in vitro experiments demonstrated that TA exerts anticancer activity against NPC by targeting the PI3K/AKT signaling pathway, leading to the suppression of cell proliferation. TA is a promising therapeutic candidate for NPC through PI3K/AKT signaling pathway. These results provide insights into the clinical application of TA, particularly when considered in combination with other therapeutic modalities.

Molecular Docking Simulation↗

Isomerization around a C=N double bond and a C=C double bond with a nitrogen atom attached: thermal and photochemical routes.

The Longuet-Higgins phase change theorem is used to show that, in certain photochemical reactions, a single product is formed via a conical intersection. The cis-trans isomerization around the double bond in the formaldiminium cation and vinylamine are shown to be possible examples. This situation is expected to hold when the reactant can be converted to the product via two distinct elementary ground-state reactions that differ in their phase characteristics. In one, the total electronic wavefunction preserves its phase in the reaction; in the other, the phase is inverted. Under these conditions, a conical intersection necessarily connects the first electronic excited state to the ground state, leading to rapid photochemical isomerization following optical excitation. Detailed quantum chemical calculations support the proposed model. The possibility that a similar mechanism is operative in other systems, among them the rapid photo-induced cis-trans isomerization of longer protonated Schiff bases (the parent chromophores of rhodopsins), is discussed.

Journal Article↗

Joule heating and heat transfer in poly(dimethylsiloxane) microfluidic systems.

Joule heating is a significant problem in electrokinetically driven microfluidic chips, particularly polymeric systems where low thermal conductivities amplify the difficulty in rejecting this internally generated heat. In this work, a combined experimental (using a microscale thermometry technique) and numerical (using a 3D "whole-chip" finite element model) approach is used to examine Joule heating and heat transfer at a microchannel intersection in poly(dimethylsiloxane)(PDMS), and hybrid PDMS/Glass microfluidic systems. In general the numerical predictions and the experimental results agree quite well (typically within +/- 3 degree C), both showing dramatic temperature gradients at the intersection. At high potential field strengths a nearly five fold increase in the maximum buffer temperature was observed in the PDMS/PDMS chips over the PDMS/Glass systems. The detailed numerical analysis revealed that the vast majority of steady state heat rejection is through lower substrate of the chip, which was significantly impeded in the former case by the lower thermal conductivity PDMS substrate. The observed higher buffer temperature also lead to a number of significant secondary effects including a near doubling of the volume flow rate. Simple guidelines are proposed for improving polymeric chip design and thereby extend the capabilities of these microfluidic systems.

Computer Simulation↗

On diabatization and the topological D-matrix: theory and numerical studies of the H + H2 system and the C2H2 molecule.

This article is divided into two main parts: (1) The theoretical part contains a new derivation of the topological matrix D (M. Baer and A. Alijah, Chem. Phys. Lett., 2000, 319, 489) which is based, solely, on the spatial dependent electronic manifold. This derivation enables more intimate relations between the adiabatic and the diabatic frameworks as is discussed in detail in the manuscript. (2) The numerical part is also divided into two parts: (a) In the first part we extend our previous study on the H + H2 system (G. Halasz, A. Vibok, A. M. Mebel and M. Baer, J. Chem. Phys., 2003, 118, 3052) by calculating the topological matrix for five states (instead of three) and for configuration spaces four times larger than before. These studies are expected to yield detailed information on the possibility of diabatization of this system. (b) We report on preliminary results concerning the C2H2 molecule. So far we established the existence of one (1,2) conical intersection and we have good reasons to believe that this system contains several (2,3) and (3,4) conical intersections as well.

Journal Article↗

Time-dependent quantum wave-packet description of the 1pi sigma* photochemistry of pyrrole.

The photoinduced hydrogen elimination reaction in pyrrole via the conical intersection of the 1B1 (1pi sigma*) excited state with the electronic ground state has been investigated by time-dependent quantum wave-packet dynamics. A two-dimensional model potential-energy surface has been constructed as a function of the NH stretching and the hydrogen out-of-plane bending mode, employing multi-reference ab initio electronic-structure methods. The branching ratio of the reactive flux at the conical intersection has been investigated in dependence on the initial vibrational state of the molecule. The results suggest that laser control of the photodissociation of pyrrole via mode-specific vibrational excitation should be possible.

Kinetics↗

Microchannel protein separation by electric field gradient focusing.

A microchannel device is presented which separates and focuses charged proteins based on electric field gradient focusing. Separation is achieved by setting a constant electroosmotic flow velocity against step changes in electrophoretic velocity. Where these two velocities are balanced for a given analyte, the analyte focuses at that point because it is driven to it from all points within the channel. We demonstrate the separation and focusing of a binary mixture of bovine serum albumin and phycoerythrin. The device is constructed of intersecting microchannels in poly(dimethylsiloxane)(PDMS) inlaid with hollow dialysis fibers. The device uses no exotic chemicals such as antibodies or synthetic ampholytes, but operates instead by purely physical means involving the independent manipulation of electrophoretic and electroosmotic velocities. One important difference between this apparatus and most other devices designed for field-gradient focusing is the injection of current at discrete intersections in the channel rather than continuously along the length of a membrane-bound separation channel.

Dimethylpolysiloxanes↗

On the site-specificity of polycarbonyl complexes in Cu/zeolites: combined experimental and DFT study.

The preferred Cu(+) sites and formation of mono-, di-, and tricarbonyl complexes in the Cu-FER were investigated at the periodic density functional theory level and by means of FTIR spectroscopy. The site-specificity of adsorption enthalpies of CO on Cu-FER and of vibrational frequencies of polycarbonyl complexes were investigated for various Cu(+) sites in Cu-FER. Large changes in the Cu(+) interaction with the zeolite framework were observed upon the formation of carbonyl complexes. The dicarbonyl complexes formed on Cu(+) in the main channel or on the intersection of the main and perpendicular channels are stable and both, adsorption enthalpies and CO stretching frequencies are not site-specific. The fraction of Cu(+) ions in the FER cage, that cannot form dicarbonyl can be determined from IR spectra (about 7% for the Cu-FER with Si/Al = 27.5 investigated here). The tricarbonyl complexes can be formed at the Cu(+) ions located at the 8-member ring window at the intersection of main and perpendicular channel. The stability of tricarbonyl complexes is very low (DeltaH degrees (0 K)>or=-4 kJ mol(-1)).

Carbon Monoxide↗

Kinetic mechanism of ATP-sulphurylase from rat chondrosarcoma.

ATP-sulphurylase catalyses the production of adenosine 5'-phosphosulphate (APS) from ATP and free sulphate with the release of PPi. APS kinase phosphorylates the APS intermediate to produce adenosine 3'-phosphate 5'-phosphosulphate (PAPS). The kinetic mechanism of rat chondrosarcoma ATP-sulphurylase was investigated by steady-state methods in the physiologically forward direction as well as the reverse direction. The sulphurylase activity was coupled to APS kinase activity in order to overcome the thermodynamic constraints of the sulphurylase reaction in the forward direction. Double-reciprocal initial-velocity plots for the forward sulphurylase intersect to the left of the ordinate for this reaction. KmATP and Kmsulphate were found to be 200 and 97 microM respectively. Chlorate, a competitive inhibitor with respect to sulphate, showed uncompetitive inhibition with respect to ATP with an apparent Ki of 1.97 mM. Steady-state data from experiments in the physiologically reverse direction also yielded double-reciprocal initial-velocity patterns that intersect to the left of the ordinate axis, with a KmAPS of 39 microM and a Kmpyrophosphate of 18 microM. The results of steady-state experiments in which Mg2+ was varied indicated that the true substrate is the MgPPi complex. An analogue of APS, adenosine 5'-[beta-methylene]phosphosulphate, was a linear inhibitor competitive with APS and non-competitive with respect to MgPPi. The simplest formal mechanism that agrees with all the data is an ordered steady-state single displacement with MgATP as the leading substrate in the forward direction and APS as the leading substrate in the reverse direction.

Adenosine Phosphosulfate↗

Relative labelling index: a novel stereological approach to test for non-random immunogold labelling of organelles and membranes on transmission electron microscopy thin sections.

Simple and efficient protocols for quantifying immunogold labelling of antigens localized in different cellular compartments (organelles or membranes) and statistically evaluating resulting labelling distributions are presented. Two key questions are addressed: (a) is compartmental labelling within an experimental group (e.g. control or treated) consistent with a random distribution? and (b) do labelling patterns vary between groups (e.g. control vs. treated)? Protocols rely on random sampling of cells and compartments. Numbers of gold particles lying on specified organelle compartments provide an observed frequency distribution. By superimposing test-point lattices on cell profiles, design-based stereology is used to determine numbers of points lying on those same compartments. Random points hit compartments with probabilities determined by their relative sizes and so provide a convenient internal standard, namely, the expected distribution if labelling is purely random. By applying test-line lattices, and counting sites at which these intersect membrane traces, analogous procedures provide observed and expected labelling distributions for different classes of membranes. Dividing observed golds by expected golds provides a relative labelling index (RLI) for each compartment and, for random labelling, the predicted RLI = 1. In contrast to labelling densities of organelles (golds microm(-2) or membranes (golds microm(-1)), RLI values are estimated without needing to know lattice constants (area per point or length per intersection) or specimen magnification. Gold distributions within a group are compared by chi-squared analysis to test if the observed distribution differs significantly from random and, if it is non-random, to identify compartments which are preferentially labelled (RLI > 1). Contingency table analysis allows labelling distributions in different groups of cells to be compared. Protocols are described and illustrated using worked specimen examples and real data.

Chi-Square Distribution↗

Evaluation of adrenal function in patients with hypothalamic and pituitary disorders: comparison of serum cortisol, urinary free cortisol and the human-corticotrophin releasing hormone test with the insulin tolerance test.

OBJECTIVE: This study aimed to evaluate the performance of screening tests (serum cortisol and 24-h urinary free cortisol) and the human-corticotrophin releasing hormone (h-CRH) test in the assessment of adrenal function in patients with hypothalamic-pituitary disorders. DESIGN: Summary receiver operating characteristics (SROC) curve analysis was applied with the insulin tolerance test (ITT) as reference test. A peak serum cortisol response to ITT > or = 500 nmol/l indicated adrenal sufficiency. The sensitivity at the intersect of the diagonal between sensitivity = 1 and (1-specificity) = 1 with the SROC curve, where sensitivity and specificity are equal, and the corresponding weighted kappa, an estimate of agreement with the ITT, served as parameters of test performance. The diagnostic yield, representing the proportion of tests obviating the need for an ITT, was also calculated. MEASUREMENTS: Serum cortisol at 0800 h (n = 122), at 1600 h (n = 116), 24-h urinary free cortisol (n = 115) and the peak serum cortisol to h-CRH (n = 129) were compared with the peak serum cortisol to ITT. PATIENTS: Eighty patients with hypothalamic-pituitary disorders in whom 75 ITT's were performed pre- and 57 post-operatively. RESULTS: Sensitivity at the intersect and weighted kappa were higher for 0800 h serum cortisol (0.873 and 0.763 respectively) than for 1600 h serum cortisol (0.769 and 0.561) and 24-h urinary free cortisol (0.777 and 0.576). These parameters were 0.868 and 0.756 for the h-CRH test. The diagnostic yield was 63.9% for 0800 h serum cortisol compared to 25.9% for 1600 h serum cortisol (P < 10(-8)), 23.5% for 24-h urinary free cortisol (P < 10(-8)) and 60.5% for the h-CRH test (NS). CONCLUSIONS: Serum cortisol measurement at 0800 h is better than 1600 h and 24-h urinary free cortisol to evaluate adrenal function in this patient category. The diagnostic applicability of the h-CRH test is not superior to 0800 h serum cortisol measurement.

Adenoma↗

2.5 kDa and 5.0 kDa heparin fragments specifically inhibit microvessel sprouting and network formation in VEGF165-mediated mammalian angiogenesis.

Tumour growth is angiogenesis dependent. Thrombosis and thromboembolism are very common in cancer patients. These patients are often treated with heparin as an anti-coagulant. Many tumour angiogens, including VEGF165, and endogenous anti-angiogenesis factors bind heparin tightly. Using the non-surgical mesenteric-window angiogenesis assay, we studied in detail the systemic effect of heparin fractions with a mean MW of 2.5, 5.0 and 16.4 kDa on the microvessel sprouting and network formation in angiogenesis mediated by VEGF165 in rats. The microvessel network was assessed objectively in terms of the number and lengths of segments (the distance between two successive branching points), the number of branching points, the degree of tortuosity, the index of interconnecting loop formation, the index of intersection, as well as the number and lengths of sprouts. Compared with the saline control, the 2.5 kDa fraction significantly shortened the microvessel sprouts and the microvessel segments but increased the microvessel tortuosity in statistical terms; the 5.0 kDa fraction statistically significantly shortened the sprouts, decreased the number of segments and the number of microvessel branching points; whereas the 16.4 kDa fraction statistically significantly elongated the longest segments. Moreover, statistically significant differences were found between the three heparin fractions in terms of microvessel tortuosity (2.5 vs. 16.4 kDa), index of loop formation (5.0 vs. 2.5 + 16.4 kDa) and index of intersection (5.0 vs. 16.4 kDa). These findings demonstrate that heparin fragments size-specifically inhibit microvessel sprouting and network formation in VEGF165-mediated angiogenesis. As VEGF165 is a potent angiogen in human tumours, we suggest that heparin enriched in 2.5 kDa species and 5.0 kDa species especially should be exploited as a combined anti-coagulant and specific adjuvant anti-angiogenic agent in cancer patients who require anti-coagulant therapy.

Angiogenesis Inhibitors↗

Estimating surface area by the isotropic fakir method from thick slices cut in an arbitrary direction.

The proposed fakir method for estimating surface area is based on counting the intersections between the surface lying within a thick slice, and an isotropic spatial grid consisting of a combination of linear probes called fakir probes. An unbiased procedure using a directly randomized spatial grid rather than sections with randomized directions is presented. The method is applicable if perfectly registered serial sections of the surface are available in a thick slice while the direction of the slice can be arbitrary. The efficiency of the fakir method using different arrangements of orthogonal triplets of fakir probes is evaluated and it is shown that mutually shifted probes are superior to non-shifted ones. The application software for interactive counting of intersections between computer-generated fakir probes and the surface within the stack of digitized images is described and demonstrated by two examples: estimation of the surface area of individual tobacco cell chains using a confocal microscope, and estimation of the total area of exposed surface of mesophyll cells in a barley leaf using a wide-field transmission microscope.

Journal Article↗

Estimation of average particle size from vertical projections.

A new stereological relationship is derived for the estimation of average size (average width) of a collection of convex particles in a 3D microstructure. The average size is estimated from measurements performed on projected images of the microstructure generated by total vertical projections. The stereological relationship is as follows: D = IC/(2N0beta). D is the average width, ;IC is the average absolute number of intersections between the specifically oriented and regularly spaced cycloid shape test lines and particle boundaries observed in the total vertical projections, N0 is the total number of particles observed in the total vertical projection and the parameter beta is a characteristic of the measurement grid; it has units of reciprocal of length. The result is applicable to any arbitrary collection of convex particles; the particle orientations need not be isotropic. Only 'intersection counts' are required; it is not necessary to measure sizes of the particles in the projected images.

Journal Article↗

Stereological length estimation using spherical probes.

Lineal structures in biological tissue support a wide variety of physiological functions, including membrane stabilization, vascular perfusion, and cell-to-cell communication. In 1953, Smith and Guttman demonstrated a stereological method to estimate the total length density (Lv) of linear objects based on random intersections with a two-dimensional sampling probe. Several methods have been developed to ensure the required isotropy of object-probe intersections, including isotropic-uniform-random (IUR) sections, vertical-uniform-random (VUR) slices, and isotropic virtual planes. The disadvantages of these methods are the requirements for inconvenient section orientations (IUR, VUR) or complex counting rules at multiple focal planes (isotropic virtual planes). To overcome these limitations we report a convenient and straightforward approach to estimate Lv and total length, L, for linear objects on tissue sections cut at any arbitrary orientation. The approach presented here uses spherical probes that are inherently isotropic, combined with unbiased fractionator sampling, to demonstrate total L estimation for thin nerve fibres in dorsal hippocampus of the mouse brain.

Animals↗

Mechanism of porcine pancreatic alpha-amylase. Inhibition of amylose and maltopentaose hydrolysis by alpha-, beta- and gamma-cyclodextrins.

The effects of alpha-, beta- and gamma-cyclodextrins on the amylose and maltopentaose hydrolysis catalysed by porcine pancreatic alpha-amylase (PPA) were investigated. The results of the statistical analysis performed on the kinetic data using the general initial velocity equation of a one-substrate reaction in the presence of one inhibitor indicate that the type of inhibition involved depends on the substrate used: the inhibition of amylose hydrolysis by alpha-, beta- and gamma-cyclodextrin is of the competitive type, while the inhibition of maltopentaose hydrolysis is of the mixed noncompetitive type. Consistently, the Lineweaver-Burk plots intersect on the vertical axis when amylose is used as the substrate, while in the case of maltopentaose, the intersection occurs at a point located in the second quadrant. The inhibition of the hydrolysis therefore involves only one abortive complex, PPA-cyclodextrin, when amylose is used as the substrate, while two abortive complexes, PPA-cyclodextrin and PPA-maltopentaose-cyclodextrin, are involved with maltopentaose. The mixed noncompetitive inhibition thus shows the existence of one accessory binding site. In any case, only one molecule of inhibitor binds to PPA. In line with these findings, the difference spectra of PPA produced by alpha-, beta- and gamma-cyclodextrin indicate that binding occurs at a tryptophan and a tyrosine residue. The corresponding dissociation constants and the inhibition constants obtained using the kinetic approach are in the same range (1.2-7 mM). The results obtained here on the inhibition of maltopentaose hydrolysis by cyclodextrin are similar to those previously obtained with acarbose as the inhibitor [Alkazaz, M., Desseaux, V., Marchis-Mouren, G., Prodanov, E. & Santimone, M. (1998) Eur. J. Biochem. 252, 100-107], but differ from those obtained with amylose as the substrate and acarbose as inhibitor [Alkazaz, M., Desseaux, V., Marchis-Mouren, G., Payan, F., Forest, E. & Santimone, M. (1996) Eur. J. Biochem. 241, 787-796]. It is concluded that the hydrolysis of both long and short chain substrates requires at least one secondary binding site, including a tryptophan residue.

Amylose↗

A new technique for establishing dry weight in hemodialysis patients via whole body bioimpedance.

BACKGROUND: Quantitative techniques are necessary to achieve dry weight (DW) in patients with kidney failure. Bioimpedance spectroscopy (BIS) is a non-invasive method that determines the volume of body fluid compartments. The current work evaluates the use of BIS data in hemodialysis patients for the prediction of DW. METHODS: A new technique has been devised for the estimation of DW that involves the intersection of two slopes, slope normovolemia (SNV) and slope hypervolemia (SHV). These slopes characterize the variation in extracellular water (ECW) with body weight (BW) in the states of normovolemia and hypervolemia, respectively. SNV was established via measurements of ECW and BW in 30 healthy subjects. In a longitudinal study in new hemodialysis patients, successive reduction of post-dialysis weight (PDW) was attempted until clinical signs of normovolemia were presented. Measurements of ECW and BW that were acquired at the beginning of each treatment were used to determine SHV. RESULTS: SNV was found to be 0.239 L/kg and 0.214 L/kg for male and female healthy subjects, respectively. A significant DeltaPDW predicted by the new method (-4.98 kg) was highly correlated to the DeltaPDW achieved in the study (-5.85 kg, R = 0.839). Blood pressure was reduced (P < 0.001) and an 86% decrease in antihypertensive agents was achieved. CONCLUSION: The method of intersecting slopes (SHV with SNV) via BIS is a new method for the prediction DW. This approach will offer considerable improvement for the routine management of DW in the dialysis setting.

Adult↗

Left and right atrial volume by freehand three-dimensional echocardiography: in vivo validation using magnetic resonance imaging.

INTRODUCTION: Measurement of left and right atrial size is important for the management of arrhythmias, valvular and congenital heart disease. We have demonstrated that freehand three-dimensional (3D) echocardiography is more accurate and reproducible than two-dimensional (2D) echocardiography for measurement of left ventricular mass and volume. However, no prior study has validated the accuracy of freehand 3D for the determination of left or right atrial volume. METHODS: End-systolic (maximum) left and right atrial volumes were determined in 21 volunteer patients and normal subjects by one, two, and freehand 3D transthoracic echocardiography and compared to volumes obtained by gradient recalled magnetic resonance imaging. Three-dimensional echocardiographic determination of atrial volume was obtained using an acoustic spatial locator, a line-of-intersection display, and a surface reconstruction algorithm. Two-dimensional echocardiographic atrial volumes were obtained from apical biplane images of the left atrium and an apical single plane image of the right atrium using a summation of disks method. One-dimensional (ID) estimates of left atrial volume were determined by cubing the M-mode ID antero-posterior dimension obtained on the parasternal long axis view. RESULTS: An excellent correlation was Obtained between freedhand 3D echocardiography and magnetic resonce imaging (MRI) for the left atrium (r = 0.90, SEE=9.6 ml) and for the right atrium (r = 0.91, SEE = 8.8 ml) with a small bias (left atrium 5.25 ml, right atrium 12.06 ml) and narrow limits of agreement (left atrium 22.14 ml, right atrium 25.54 ml). Two-dimensional echocardiography correlated less well (left atrium r = 0.87, SEE = 10.23 ml, right atrium r = 0.79, SEE = 19.74 ml), and had a higher bias (left atrium 14.46 ml, right atrium 8.99 ml) and larger limits of agreement (left atrium 24.37 ml, right atrium 41.16 ml). One-dimensional estimates of left atrial volume correlated poorly with magnetic resonance determined left atrial volume (r = 0.80, SEE = 6.61 ml) and had unacceptably high bias (45.09 ml) and limits of agreement (35.52 ml). Interobserver variability was lowest for 3D echocardiography (left atrium 7.2 ml, 11%, right atrium 8.7 ml, 16%). CONCLUSIONS: Freehand 3D echocardiography using the line of intersection display for guidance of image positioning and a polyhedral surface reconstruction algorithm is a valid, accurate, reproducible method for determining left and right atrial volume in humans that is comparable to magnetic resonance imaging and is superior to current ID and 2D echocardiographic techniques.

Adult↗