Self-organizing maps and molecular similarity

Self-organizing maps generated by Kohonen neural networks provide a method for transforming multidimensional problems into lower dimensional problems. Here, a Kohonen network is used to generate two-dimensional representations of the electrostatic potential about the ring structures of histamine H2 agonists. Previous work by J. Gasteiger and X. Li (Angew. Chem. Int. Ed. Engl. 1994, 33, 643) has shown the usefulness of such a method for classifying molecules as muscarinic or nicotinic agonists. Here, the method is extended to rank histamine H2 agonists in order of biological activity.     

Encoding of Natural Sounds at Multiple Spectral and Temporal Resolutions in the Human Auditory Cortex

Functional neuroimaging research provides detailed observations of the response patterns that natural sounds (e.g. human voices and speech, animal cries, environmental sounds) evoke in the human brain. The computational and representational mechanisms underlying these observations, however, remain largely unknown. Here we combine high spatial resolution (3 and 7 Tesla) functional magnetic resonance imaging (fMRI) with computational modeling to reveal how natural sounds are represented in the human brain. We compare competing models of sound representations and select the model that most accurately predicts fMRI response patterns to natural sounds. Our results show that the cortical encoding of natural sounds entails the formation of multiple representations of sound spectrograms with different degrees of spectral and temporal resolution. The cortex derives these multi-resolution representations through frequency-specific neural processing channels and through the combined analysis of the spectral and temporal modulations in the spectrogram. Furthermore, our findings suggest that a spectral-temporal resolution trade-off may govern the modulation tuning of neuronal populations throughout the auditory cortex. Specifically, our fMRI results suggest that neuronal populations in posterior/dorsal auditory regions preferably encode coarse spectral information with high temporal precision. Vice-versa, neuronal populations in anterior/ventral auditory regions preferably encode fine-grained spectral information with low temporal precision. We propose that such a multi-resolution analysis may be crucially relevant for flexible and behaviorally-relevant sound processing and may constitute one of the computational underpinnings of functional specialization in auditory cortex.     

Progress in developing a new detection method for the harmful algal bloom species,Karenia brevis,through multiwavelength spectroscopy

Multiwavelength spectroscopy is a rapid analytical technique that can be applied to detect, identify, and quantify microorganisms such as Karenia brevis, the species known for frequent red-tide blooms in Florida's coastal waters. This research will report on a model-based interpretation of UV–vis spectra of K. brevis. The spectroscopy models are based on light scattering and absorption theories, and the approximation of the frequency-dependant optical properties of the basic constituents of living organisms. Absorption and scattering properties of K. brevis, such as cell size/shape, internal structure, and chemical composition, are shown to predict the spectral features observed in the measured spectra. The parameters for the interpretation model were based upon both reported literature values, and experimental values obtained from live cultures and pigment standards. Measured and mathematically derived spectra were compared to determine the adequacy of the model, contribute new spectral information, and to establish the proposed spectral interpretation approach as a new detection method for K. brevis.     

Quantitative gas-liquid chromatography and mass spectrometry of the N(O)-perfluorobutyryl-O-isoamyl derivatives of amino acids.

A modification of a gas-liquid chromatographic method for quantitative analysis of amino acids as the N(O)-perfluorobutyryl-O-isoamyl derivatives is described. The modifications include changes in time and temperature for esterification, improved preparation of the esterification reagents and conducting the derivatizations in vacuo to obtain reproducible values for amino acids such as methionine and arginine. Mass spectral data are presented for all the derivatized amino acids.     

High-Resolution Two-Dimensional J-Resolved NMR Spectroscopy for Biological Systems

NMR spectroscopy is a principal tool in metabolomic studies and can, in theory, yield atom-level information critical for understanding biological systems. Nevertheless, NMR investigations on biological tissues generally have to contend with field inhomogeneities originating from variations in macroscopic magnetic susceptibility; these field inhomogeneities broaden spectral lines and thereby obscure metabolite signals. The congestion in one-dimensional NMR spectra of biological tissues often leads to ambiguities in metabolite identification and quantification. We propose an NMR approach based on intermolecular double-quantum coherences to recover high-resolution two-dimensional (2D) J-resolved spectra from inhomogeneous magnetic fields, such as those created by susceptibility variations in intact biological tissues. The proposed method makes it possible to acquire high-resolution 2D J-resolved spectra on intact biological samples without recourse to time-consuming shimming procedures or the use of specialized hardware, such as magic-angle-spinning probes. Separation of chemical shifts and J couplings along two distinct dimensions is achieved, which reduces spectral crowding and increases metabolite specificity. Moreover, the apparent J coupling constants observed are magnified by a factor of 3, facilitating the accurate measurement of small J couplings, which is useful in metabolic analyses. Dramatically improved spectral resolution is demonstrated in our applications of the technique on pig brain tissues. The resulting spectra contain a wealth of chemical shift and J-coupling information that is invaluable for metabolite analyses. A spatially localized experiment applied on an intact fish (Crossocheilus siamensis) reveals the promise of the proposed method in in vivo metabolite studies. Moreover, the proposed method makes few demands on spectrometer hardware and therefore constitutes a convenient and effective manner for metabonomics study of biological systems.     

The Time Course of Activation of Object Shape and Shape+Colour Representations during Memory Retrieval

Little is known about the timing of activating memory for objects and their associated perceptual properties, such as colour, and yet this is important for theories of human cognition. We investigated the time course associated with early cognitive processes related to the activation of object shape and object shape+colour representations respectively, during memory retrieval as assessed by repetition priming in an event-related potential (ERP) study. The main findings were as follows: (1) we identified a unique early modulation of mean ERP amplitude during the N1 that was associated with the activation of object shape independently of colour; (2) we also found a subsequent early P2 modulation of mean amplitude over the same electrode clusters associated with the activation of object shape+colour representations; (3) these findings were apparent across both familiar (i.e., correctly coloured – yellow banana) and novel (i.e., incorrectly coloured - blue strawberry) objects; and (4) neither of the modulations of mean ERP amplitude were evident during the P3. Together the findings delineate the timing of object shape and colour memory systems and support the notion that perceptual representations of object shape mediate the retrieval of temporary shape+colour representations for familiar and novel objects.     

High-Resolution Two-Dimensional J-Resolved NMR Spectroscopy for Biological Systems

NMR spectroscopy is a principal tool in metabolomic studies and can, in theory, yield atom-level information critical for understanding biological systems. Nevertheless, NMR investigations on biological tissues generally have to contend with field inhomogeneities originating from variations in macroscopic magnetic susceptibility; these field inhomogeneities broaden spectral lines and thereby obscure metabolite signals. The congestion in one-dimensional NMR spectra of biological tissues often leads to ambiguities in metabolite identification and quantification. We propose an NMR approach based on intermolecular double-quantum coherences to recover high-resolution two-dimensional (2D) J-resolved spectra from inhomogeneous magnetic fields, such as those created by susceptibility variations in intact biological tissues. The proposed method makes it possible to acquire high-resolution 2D J-resolved spectra on intact biological samples without recourse to time-consuming shimming procedures or the use of specialized hardware, such as magic-angle-spinning probes. Separation of chemical shifts and J couplings along two distinct dimensions is achieved, which reduces spectral crowding and increases metabolite specificity. Moreover, the apparent J coupling constants observed are magnified by a factor of 3, facilitating the accurate measurement of small J couplings, which is useful in metabolic analyses. Dramatically improved spectral resolution is demonstrated in our applications of the technique on pig brain tissues. The resulting spectra contain a wealth of chemical shift and J-coupling information that is invaluable for metabolite analyses. A spatially localized experiment applied on an intact fish (Crossocheilus siamensis) reveals the promise of the proposed method in in vivo metabolite studies. Moreover, the proposed method makes few demands on spectrometer hardware and therefore constitutes a convenient and effective manner for metabonomics study of biological systems.     

Measurements of membrane potentials in plant mitochondria with the safranine method

The positively charged dye, safranine, has been used as an indicator of membrane potentials in mung bean (Phaseolus aureus) and Voodoo lily (Sauromatum guttatum) mitochondria under a variety of metabolic conditions. The spectral response of safranine has been calibrated with respect to a K⁺ diffusion potential and was found to be linearly related to the developed potential within the range of 50 to 160 millivolts. Both respiration and ATP hydrolysis gave rise to a membrane potential of approximately 135 millivolts. Respiratory inhibitors such as cyanide and antimycin depolarized the potential, whereas rotenone has little effect. No potentials were developed during NADH supported cyanide insensitive respiration. It is concluded that safranine may be a useful spectrophotometric probe of the mitochondrial membrane potential.     

Electrical Properties of the Pacemaker Neurons in the Heart Ganglion of a Stomatopod, Squilla oratoria

In the Squilla heart ganglion, the pacemaker is located in the rostral group of cells. After spontaneous firing ceased, the electrophysiological properties of these cells were examined with intracellular electrodes. Cells respond to electrical stimuli with all-or-none action potentials. Direct stimulation by strong currents decreases the size of action potentials. Comparison with action potentials caused by axonal stimulation and analysis of time relations indicate that with stronger currents the soma membrane is directly stimulated whereas with weaker currents the impulse first arises in the axon and then invades the soma. Spikes evoked in a neuron spread into all other neurons. Adjacent cells are interconnected by electrotonic connections. Histologically axons are tied with the side-junction. B spikes of adjacent cells are blocked simultaneously by hyperpolarization or by repetitive stimulation. Experiments show that under such circumstances the B spike is not directly elicited from the A spike but is evoked by invasion of an impulse or electrotonic potential from adjacent cells. On rostral stimulation a small prepotential precedes the main spike. It is interpreted as an action potential from dendrites.     

Coupling single base extension to a spectral codification tool for increased throughput screening

We report a new strategy that combines a Förster Resonance Energy Transfer (FRET) based spectral codification tool with a single base extension (SBE) reaction for rapid and medium-throughput analysis of single nucleotide polymorphisms (SNPs). This strategy is based on the spectral codification - a donor (fluorophore labeled probe complementary to the region adjacent to an SNP) is used to induce specific FRET signatures from an acceptor fluorophore revealing the SNP variant. Using an SBE reaction and differently labeled ddNTPs, we can directly question each donor probe and retrieve information about which allele variant is present at that locus. The potential of the method is demonstrated by application to simultaneous questioning of two loci in the same reaction tube. Following calibration with all possible combinations of FRET pairs, an evaluation algorithm was calibrated so as to optimize base calling and allow unequivocal allele scoring with more than 80% confidence (for two simultaneous loci being questioned, one homo- and one heterozygous). In conclusion, this spectral codification approach may constitute a solution towards increasing throughput capability of single base extension based assays.     

The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information

In auditory cortex, temporal information within a sound is represented by two complementary neural codes: a temporal representation based on stimulus-locked firing and a rate representation, where discharge rate co-varies with the timing between acoustic events but lacks a stimulus-synchronized response. Using a computational neuronal model, we find that stimulus-locked responses are generated when sound-evoked excitation is combined with strong, delayed inhibition. In contrast to this, a non-synchronized rate representation is generated when the net excitation evoked by the sound is weak, which occurs when excitation is coincident and balanced with inhibition. Using single-unit recordings from awake marmosets (Callithrix jacchus), we validate several model predictions, including differences in the temporal fidelity, discharge rates and temporal dynamics of stimulus-evoked responses between neurons with rate and temporal representations. Together these data suggest that feedforward inhibition provides a parsimonious explanation of the neural coding dichotomy observed in auditory cortex.     

Psychophysiological and Some Functional Markers of Mental Workload in Young Men

The emotional state of a person affects both the central level and the peripheral indices of the autonomic nervous system, particularly those of the regulation of the heart rate. Our study showed that boys with a higher level of anxiety had higher values of the latent period of the P300 evoked potential and lower indices of short-term auditory memory. Changes in the temporal and spectral components of heart rate variability under the conditions of mental workload indicate that the neurohumoral regulation of the heart rate is shifted toward the suprasegmental influences, including pituitary–hypothalamic and cortical influences.     

噪声对豚鼠耳蜗电图功率谱的影响

本文对豚鼠噪声暴露后的耳蜗电图功率谱进行了分析,实验表明:噪声组豚鼠耳蜗电图功率谱150～300Hz频段能量较正常组有明显增长;500～850Hz和850～1400Hz频段能量不集中(表2).另外,噪声组耳蜗电图功率谱与标准型的相关度比正常组与标准型的相关度差(P<0.01).     

Titles of related papers in other sections

A method is described for isolation of the Rhodopseudomonas viridis reaction center complex free of altered, 685 nm absorbing pigment. This improved preparation contains two c-type cytochromes in the ratio P-960: cytochrome c-558: cytochrome c-553 of 1 : 2 : 2 to 3. The near infrared spectral forms of the reduced preparation are located at 790, 832, 846 and 987 nm at 77 K; the oxidized complex absorbs at 790, 808, 829 and approx. 1310 nm. The 790 nm band is attributed to bacteriophaeophytin b and the other absorbances to bacteriochlorophyll b. The visible absorption bands may be assigned to these pigments and to the cytochromes present and, probably, to a carotenoid. The presence of two bacteriochlorophyll b spectral forms in the P⁺-830 band suggests that exciton interactions occur among pigments in the oxidized, as well as the reduced, reaction center. Changes in the 790 and 544 nm bands upon illumination of the reaction center preparation at low redox potential may be indicative of a role for bacteriophaeophytin b in primary photochemical events.     

Motor organization of the lateral cerebellar nucleus of the rat

The motor organization of the nucleus lateralis (NL) of the cerebellum of the rat was investigated by studying the motor effects following the electrical microstimulation. The movements evoked by the NL stimulation concerned prevalently the forelimb and the head segments. The movements of the hindlimb segments were evoked in only few cases. The NL is organized as a mosaic of zones without, or at least very little overlap. The various body segments are differently represented in the NL. Some of them are once represented (single representations). In other cases, the same movements were evoked by different NL regions (multiple representations). Finally, in a last lot of cases, various representations concerned the same body regions but from each representation a different type of movement was evoked (specific representations, i.e. displacement of an individual digit and flexion of all digits together). The topographical distribution of the representations in the NL cytological regions (magnicellularis, NLm; dorsolateral hump, DLH; subnucleus lateralis parvocellularis, slp) suggests the idea that each of them may be concerned in a specific motor activity: the NLm would control the position of the body, or of part of it, in the space; the DLH would be concerned in the oral (prevalently) and in the forelimb motor activity; the slp would be concerned in the exploration of the environment as well as in skilled movements of the distalmost forelimb segments.     

Classification of electrocardiogram signals with support vector machines and genetic algorithms using power spectral features

This paper proposes a new power spectral-based hybrid genetic algorithm-support vector machines (SVMGA) technique to classify five types of electrocardiogram (ECG) beats, namely normal beats and four manifestations of heart arrhythmia. This method employs three modules: a feature extraction module, a classification module and an optimization module. Feature extraction module extracts electrocardiogram's spectral and three timing interval features. Non-parametric power spectral density (PSD) estimation methods are used to extract spectral features. Support vector machine (SVM) is employed as a classifier to recognize the ECG beats. We investigate and compare two such classification approaches. First they are specified experimentally by the trial and error method. In the second technique the approach optimizes the relevant parameters through an intelligent algorithm. These parameters are: Gaussian radial basis function (GRBF) kernel parameter σ and C penalty parameter of SVM classifier. Then their performances in classification of ECG signals are evaluated for eight files obtained from the MIT–BIH arrhythmia database. Classification accuracy of the SVMGA approach proves superior to that of the SVM which has constant and manually extracted parameter.     

Responses of the Smooth Muscle Membrane of Guinea Pig Jejunum Elicited by Field Stimulation

Field stimulation of the jejunum elicited successively an action potential of spike form, a slow excitatory depolarization, a slow inhibitory hyperpolarization, and a postinhibitory depolarization as a rebound excitation. The slow depolarization often triggered the spike. The inhibitory potential showed lower threshold than did the excitatory potential. Both the excitatory potentials were abolished by atropine and tetrodotoxin. Effective membrane resistance measured by the intracellular polarizing method was reduced during the peak of the excitatory potential, but the degree of reduction was smaller than that evoked by iontophoretic application of acetylcholine. Conditioning hyperpolarization of the muscle membrane modified the amplitude of the excitatory potential. The estimated reversal potential level for the excitatory potenialt was about 0 mv. No changes could be observed in the amplitude of the inhibitory potential when hyperpolarization was induced with intracellularly applied current. Low [K]_o and [Ca]_o blocked the generation of the excitatory potential but the amplitude of the inhibitory potential was enhanced in low [K]_o. Low [Ca]_o and high [Mg]_o had no effect on the inhibitory potential.     

Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials

Background

There are several common ways to encode a tree as a matrix, such as the adjacency matrix, the Laplacian matrix (that is, the infinitesimal generator of the natural random walk), and the matrix of pairwise distances between leaves. Such representations involve a specific labeling of the vertices or at least the leaves, and so it is natural to attempt to identify trees by some feature of the associated matrices that is invariant under relabeling. An obvious candidate is the spectrum of eigenvalues (or, equivalently, the characteristic polynomial).

Results

We show for any of these choices of matrix that the fraction of binary trees with a unique spectrum goes to zero as the number of leaves goes to infinity. We investigate the rate of convergence of the above fraction to zero using numerical methods. For the adjacency and Laplacian matrices, we show that the a priori more informative immanantal polynomials have no greater power to distinguish between trees.

Conclusion

Our results show that a generic large binary tree is highly unlikely to be identified uniquely by common spectral invariants.     

Representation of spectrotemporal sound information in the ascending auditory pathway

The representation of sound information in the central nervous system relies on the analysis of time-varying features in communication and other environmental sounds. How are auditory physiologists and theoreticians to choose an appropriate method for characterizing spectral and temporal acoustic feature representations in single neurons and neural populations? A brief survey of currently available scientific methods and their potential usefulness is given, with a focus on the strengths and weaknesses of using noise analysis techniques for approximating spectrotemporal response fields (STRFs). Noise analysis has been used to foster several conceptual advances in describing neural acoustic feature representation in a variety of species and auditory nuclei. STRFs have been used to quantitatively assess spectral and temporal transformations across mutually connected auditory nuclei, to identify neuronal interactions between spectral and temporal sound dimensions, and to compare linear vs. nonlinear response properties through state-dependent comparisons. We propose that noise analysis techniques used in combination with novel stimulus paradigms and parametric experiment designs will provide powerful means of exploring acoustic feature representations in the central nervous system.