Automatic analysis of composite physical signals using non-negative factorization and information criterion

In time-resolved spectroscopy, composite signal sequences representing energy transfer in fluorescence materials are measured, and the physical characteristics of the materials are analyzed. Each signal sequence is represented by a sum of non-negative signal components, which are expressed by model functions. For analyzing the physical characteristics of a measured signal sequence, the parameters of the model functions are estimated. Furthermore, in order to quantitatively analyze real measurement data and to reduce the risk of improper decisions, it is necessary to obtain the statistical characteristics from several sequences rather than just a single sequence. In the present paper, we propose an automatic method by which to analyze composite signals using non-negative factorization and an information criterion. The proposed method decomposes the composite signal sequences using non-negative factorization subjected to parametric base functions. The number of components (i.e., rank) is also estimated using Akaike's information criterion. Experiments using simulated and real data reveal that the proposed method automatically estimates the acceptable ranks and parameters.     

Issues in the classification of multimodal communication signals

Communication involves complex behavior in multiple sensory channels, or "modalities." We provide an overview of multimodal communication and its costs and benefits, place examples of signals and displays from an array of taxa, sensory systems, and functions into our signal classification system, and consider issues surrounding the categorization of multimodal signals. The broadest level of classification is between signals with redundant and nonredundant components, with finer distinctions in each category. We recommend that researchers gather information on responses to each component of a multimodal signal as well as the response to the signal as a whole. We discuss the choice of categories, whether to categorize signals on the basis of the signal or the response, and how to classify signals if data are missing. The choice of behavioral assay may influence the outcome, as may the context of the communicative event. We also consider similarities and differences between multimodal and unimodal composite signals and signals that are sequentially, rather than simultaneously, multimodal.     

Independent sources of condition dependency and multiple pathways determine a composite trait: lessons from carotenoid‐based plumage colouration

Many colour ornaments are composite traits consisting of at least four components, which themselves may be more complex, determined by independent evolutionary pathways, and potentially being under different environmental control. To date, little evidence exists that several different components of colour elaboration are condition dependent and no direct evidence exists that different ornamental components are affected by different sources of variation. For example, in carotenoid‐based plumage colouration, one of the best‐known condition‐dependent ornaments, colour elaboration stems from both condition‐dependent pigment concentration and structural components. Some environmental flexibility of these components has been suggested, but specifically which and how they are affected remains unknown. Here, we tested whether multiple colour components may be condition dependent, by using a comprehensive 3 × 2 experimental design, in which we carotenoid supplemented and immune challenged great tit nestlings (Parus major) and quantified effects on different components of colouration. Plumage colouration was affected by an interaction between carotenoid availability and immune challenge. Path analyses showed that carotenoid supplementation increased plumage saturation via feather carotenoid concentration and via mechanisms unrelated to carotenoid deposition, while immune challenge affected feather length, but not carotenoid concentration. Thus, independent condition‐dependent pathways, affected by different sources of variation, determine colour elaboration. This provides opportunities for the evolution of multiple signals within components of ornamental traits. This finding indicates that the selective forces shaping the evolution of different components of a composite trait and the trait's signal content may be more complex than believed so far, and that holistic approaches are required for drawing comprehensive evolutionary conclusions.     

Finding composite regulatory patterns in DNA sequences

Pattern discovery in unaligned DNA sequences is a fundamental problem in computational biology with important applications in finding regulatory signals. Current approaches to pattern discovery focus on monad patterns that correspond to relatively short contiguous strings. However, many of the actual regulatory signals are composite patterns that are groups of monad patterns that occur near each other. A difficulty in discovering composite patterns is that one or both of the component monad patterns in the group may be 'too weak'. Since the traditional monad-based motif finding algorithms usually output one (or a few) high scoring patterns, they often fail to find composite regulatory signals consisting of weak monad parts. In this paper, we present a MITRA (MIsmatch TRee Algorithm) approach for discovering composite signals. We demonstrate that MITRA performs well for both monad and composite patterns by presenting experiments over biological and synthetic data.     

Extraction of near-field fluorescence from composite signals to provide high resolution images of glial cells

The subdiffraction optical resolution that can be achieved using near-field optical microscopy has the potential to permit new approaches and insights into subcellular function and molecular dynamics. Despite the potential of this technology, it has been difficult to apply to cellular samples. One significant problem is that sample thickness causes the optical information to be comprised of a composite signal containing both near- and far-field fluorescence. To overcome this issue we have developed an approach in which a near-field optical fiber is translated toward the cell surface. The increase in fluorescence intensity during z-translation contains two components: a far-field fluorescence signal when the tip of the fiber is distant from the labeled cell, and combined near- and far-field fluorescence when the tip interacts with the cell surface. By fitting a regression curve to the far-field fluorescence intensity as the illumination aperture approaches the cell, it is possible to isolate near-field from far-field fluorescent signals. We demonstrate the ability to resolve actin filaments in chemically fixed, hydrated glial cells. A comparison of composite fluorescence signals with extracted near-field fluorescence demonstrates that this approach significantly increases the ability to detect subcellular structures at subdiffraction resolution.     

空间独立成分分析实现fMRI信号的盲分离

独立成分分析（ICA）在功能核磁共振成像（fMRI)技术中的应用是近年来人们关注的一个热点。简要介绍了空间独立成分分析（SICA）的模型和方法,将fMRI信号分析看作是一种盲源分离问题,用快速算法实现fMRI信号的盲源分离。对fMRI信号的研究大多是在假定已知事件相关时间过程曲线的情况下,利用相关性分析得到脑的激活区域。在不清楚有哪几种因素对fMRI信号有贡献、也不清楚其时间过程曲线的情况下,用SICA可以对fMRI信号进行盲源分离,提取不同独立成分得到任务相关成分、头动成分、瞬时任务相关成分、噪声干扰、以及其它产生fMRI信号的多种源信号。     

EMG signal decomposition: how can it be accomplished and used?

Electromyographic (EMG) signals are composed of the superposition of the activity of individual motor units. Techniques exist for the decomposition of an EMG signal into its constituent components. Following is a review and explanation of the techniques that have been used to decompose EMG signals. Before describing the decomposition techniques, the fundamental composition of EMG signals is explained and after, potential sources of information from and various uses of decomposed EMG signals are described.     

Experimental evolution of a pheromone signal

Sexual signals are important in speciation, but understanding their evolution is complex as these signals are often composed of multiple, genetically interdependent components. To understand how signals evolve, we thus need to consider selection responses in multiple components and account for the genetic correlations among components. One intriguing possibility is that selection changes the genetic covariance structure of a multicomponent signal in a way that facilitates a response to selection. However, this hypothesis remains largely untested empirically. In this study, we investigate the evolutionary response of the multicomponent female sex pheromone blend of the moth Heliothis subflexa to 10 generations of artificial selection. We observed a selection response of about three‐quarters of a phenotypic standard deviation in the components under selection. Interestingly, other pheromone components that are biochemically and genetically linked to the components under selection did not change. We also found that after the onset of selection, the genetic covariance structure diverged, resulting in the disassociation of components under selection and components not under selection across the first two genetic principle components. Our findings provide rare empirical support for an intriguing mechanism by which a sexual signal can respond to selection without possible constraints from indirect selection responses.     

Components of cytochrome c oxidase detectable by EPR spectroscopy

A procedure for the preparation from frozen beef heart mitochondria of cytochrome c oxidase (EC 1.9.3.1) of high heme ( 14 μmoles/mg protein) and low extraneous copper ( 1.1 atoms Cu/mole heme) and low lipid ( 0.05 g phospholipid/g protein) content is described. EPR signals observed with the enzyme between 6 and 100 °K at various states of oxidation and at different conditions of pH and presence of solutes are described in detail. The quantities of paramagnetic species represented by these signals are estimated. Under no conditions does the sum of the EPR detectable species represent more than approx. 50% of the potentially paramagnetic components of the enzyme. Comparisons are made to the corresponding signals as observed in whole tissue, mitochondria and submitochondrial particles from a number of species. The assignment of the observed signals to known components of cytochrome c oxidase is discussed briefly.     

Separation of propagating and non propagating components in surface EMG

Surface electromyogram (EMG) detected by electrode arrays along the muscle fibre direction can be approximated by the sum of propagating and non propagating components. A technique to separate propagating and non propagating components in surface EMG signals is developed. The first step is an adaptive filter, which allows obtaining an estimation of the delay between signals detected at different channels and a first estimate of propagating and non propagating components; the second step is used to optimise the estimation of the two components. The method is applicable to signals with one propagating and one non propagating component. It was optimised on simulated signals, and then applied to single motor unit action potentials (MUAP) and to electrically elicited EMG (M-waves).

The new method was first tested on phenomenological signals constituted by the sum of a propagating and a non propagating signal and then applied to simulated and experimental EMG signals. Simulated signals were generated by a cylindrical, layered volume conductor model. Experimental signals were monopolar surface EMG signals collected from the abductor pollicis brevis muscle and M-waves recorded during transcutaneous electrical stimulation of the biceps muscle. The technique may find different applications: in single motor unit (MU) studies (a) for decreasing the variability and bias of CV estimates due to the presence of the non propagating components, (b) for estimating automatically the length of the muscle fibres from only three detected channels and (c) for removal of the stimulation artifact M-waves.     

Electron spin echo studies on chloroplasts. Spectral characteristics of electron transport components and light-induced transients

Electron-spin resonance echoes are used to study the complex overlapping ESR spectra of whole chloroplasts. By varying the repetition rate of the microwave pulse sequence, delay time, and pulse width, signals with different longitudinal and transverse relaxation times were extracted. We have identified the echo signals due to plastocyanin and ferredoxins. In addition, we have found a strong signal at g = 4.3, that possibly arises from distorted cytochrome, and weak signals in the region g = 6-9. The strong echo signal at g = 2.0047 (Signal II), is made up of at least three "dark" components that differ in their relaxation times. Upon illumination at 1.2 K several of the echo signals including Signal II show reversible light-induced components. The kinetics of these transients depend on the addition of 3(3,4-dichlorophenyl)-1,1-dimethyl urea. Part of the transients are believed to arise from cyclic electron flow around Photosystem I.     

Receiver psychology and the evolution of multicomponent signals

Many animals produce and respond to signals made up of multiple components. For example, many avian sexual displays are highly extravagant combinations of visual and acoustic elements, and are described as being 'multicomponent'. One possible reason for the evolution of such complex signals is that they provide more reliable information for receivers. However, receivers also influence signal evolution in another important way, by how they perceive and process signals: signallers will be selected to produce signals that are more easily received. The potential role of receiver psychology in the evolution of multicomponent signals has not previously been considered; in this review I present psychological results that support the notion that two components are better received than one alone. Detection can be improved by producing two components together, thus reducing the reaction time, increasing the probability of detection and lowering the intensity at which detection occurs. Discriminability of multicomponent stimuli is also made easier through better recognition, faster discrimination learning and multidimensional generalization. In addition, multicomponent stimuli also improve associative learning. I show that multicomponency does indeed improve signal reception in receivers, although the benefits of producing components in two sensory modalities (bimodal multicomponent signals) may be larger and more robust than producing them in just one (unimodal multicomponent signals). This highlights the need for consideration of receiver psychology in the evolution of multicomponent signals, and suggests that where signal components do not appear to be informative, they may instead be performing an important psychological function. Copyright 1999 The Association for the Study of Animal Behaviour.     

Diffusion in Pseudomonas aeruginosa biofilms: a pulsed field gradient NMR study

A Pseudomonas aeruginosa biofilm is studied with pulsed field gradient echo nuclear magnetic resonance. Although not all spectral components are assigned yet, the experimental results show that a biofilm consists of components with very different diffusion coefficients. The various biofilm components that give motionally narrowed 1H NMR signals, can be grouped into five classes with diffusion coefficients, ranging from 2 x 10(-9) to 1 x 10(-13) m2 s-1. Investigation of the diffusion behavior of water in the biofilm shows three fractions with different diffusion coefficients. Besides the highly mobile bulk water at least two other fractions with much lower diffusion coefficients are detected. It is shown that one of the fractions with the low diffusion coefficient probably arises from intracellular water. Also for another component of the biofilm, glycerol, three fractions with diffusion coefficients that differ more than a factor ten are detected. Also a group of signals exists which result from practically immobile components.     

新的独立成分分析算法实现功能磁共振成像信号的盲分离

采用独立成分分析(independent component analysis,ICA)的一种新的牛顿型算法来提取功能磁共振成像(functional magnetic rasonance imaging,fMRI)信号中的各种独立成分(包括与实验设计相关的成分以及各种噪声)。与fastICA相比,该算法减少了运算量,提高了运算速度,而且能够很好地分离出各个独立成分。结果表明该算法是一种有效的fMRI信号分析手段。     

Segmentation of cardiac sound signals by removing murmurs using constrained tunable-Q wavelet transform

The automatic segmentation of cardiac sound signals into heart beat cycles is generally required for the diagnosis of heart valve disorders. In this paper, a new method for segmentation of the cardiac sound signals using tunable-Q wavelet transform (TQWT) has been presented. The murmurs from cardiac sound signals are removed by suitably constraining TQWT based decomposition and reconstruction. The Q-factor, redundancy parameter and number of stages of decomposition of the TQWT are adapted to the desired statistical properties of the murmur-free reconstructed cardiac sound signals. The envelope based on cardiac sound characteristic waveform (CSCW) is extracted after the removal of low energy components from the reconstructed cardiac sound signals. Then the heart beat cycles are derived from the original cardiac sound signals by mapping the required timing information of CSCW which is obtained using established methods. The experimental results are included in order to show the effectiveness of the proposed method for segmentation of cardiac sound signals in comparison with other existing methods for various clinical cases.     

Dynamics of the ganglion cell response in the catfish and frog retinas

Responses were evoked from ganglion cells in catfish and frog retinas by a Gaussian modulation of the mean luminance. An algorithm was devised to decompose intracellularly recorded responses into the slow and spike components and to extract the time of occurrence of a spike discharge. The dynamics of both signals were analyzed in terms of a series of first-through third-order kernels obtained by cross-correlating the slow (analog) or spike (discrete or point process) signals against the white-noise input. We found that, in the catfish, (a) the slow signals were composed mostly of postsynaptic potentials, (b) their linear components reflected the dynamics found in bipolar cells or in the linear response component of type-N (sustained) amacrine cells, and (c) their nonlinear components were similar to those found in either type-N or type-C (transient) amacrine cells. A comparison of the dynamics of slow and spike signals showed that the characteristic linear and nonlinear dynamics of slow signals were encoded into a spike train, which could be recovered through the cross-correlation between the white-noise input and the spike (point process signals. In addition, well-defined spike correlates could predict the observed slow potentials. In the spike discharges from frog ganglion cells, the linear (or first-order) kernels were all inhibitory, whereas the second-order kernels had characteristics of on-off transient excitation. The transient and sustained amacrine cells similar to those found in catfish retina were the sources of the nonlinear excitation. We conclude that bipolar cells and possibly the linear part of the type-N cell response are the source of linear, either excitatory or inhibitory, components of the ganglion cell responses, whereas amacrine cells are the source of the cells' static nonlinearity.     

Morphological and histochemical comparison of the cells elicited by ectopic bone implants and tibial osteoclasts.

Pellets of mineralized and demineralized bone and a composite mixture of mineralized and demineralized, devitalized bone particles were implanted subcutaneously on the dorsal body wall of young adult rats. Two weeks post-implantation, the pellets were removed and processed for histochemical and morphological analyses. Rat proximal tibia was also processed for evaluation. The levels of tartrate-resistant acid phosphatase (TRAP) activity in the multinucleated giant cells (MNGCs) from each of the three implants and from osteoclasts were assessed using an image analyzer. The osteoclasts from the proximal tibia and the majority of MNGCs from the demineralized implants demonstrated high levels of TRAP activity. MNGCs from the mineralized implants showed either a low level or absence of TRAP activity. Most MNGCs from the composite implants exhibited a low level of TRAP activity; however, there was a population of cells that demonstrated a high level of reaction product, similar to that seen in the tibia and demineralized implant. Morphologically, osteoclasts from the proximal tibia and from the osteogenic demineralized implant exhibited ruffled borders. A small population of MNGCs from the composite implant also revealed osteoclastic features. In summary, MNGCs from the mineralized implant did not exhibit a level of TRAP reaction product or morphology similar to osteoclasts, while the majority of cells from the demineralized implant and a subpopulation of the MNGCs elicited by the composite implant did demonstrate TRAP expression and morphology similar to osteoclasts. The expression of osteoclastic characteristics in cells at an ectopic site may be dependent on accessory signals from the skeletal microenvironment; such signals appear to be absent from or incomplete in the mineralized implants but appear to be present when demineralized bone particles are implanted.     

Role of extracellular matrix and YAP/TAZ in cell fate determination

The mechanical signals transduced from cellular microenvironment can regulate cell shape and affect cell fate determination. However, how these mechanical signals are transduced to regulate biological processes of cells has remained elusive. Recent studies had elucidated a novel mechanism through which the interactions between mechanical signals from extracellular matrix and cell behavior regulation converged on the function of core components in Hippo signaling pathway, including YAP and TAZ in mammals. Moreover, several very recent studies have found a new crosstalk between Wnt and Hippo signaling in the regulation of cell fate determination. Such mechanism may explain how mechanical signals from microenvironment can regulate cell behavior and determine cell fate.     

A dissection model for mapping complex traits

Many quantitative traits are composites of other traits that contribute differentially to genetic variation. Quantitative trait locus (QTL) mapping of these composite traits can benefit by incorporating the mechanistic process of how their formation is mediated by the underlying components. We propose a dissection model by which to map these interconnected components traits under a joint likelihood setting. The model can test how a composite trait is determined by pleiotropic QTLs for its component traits or jointly by different sets of QTLs each responsible for a different component. The model can visualize the pattern of time‐varying genetic effects for individual components and their impacts on composite traits. The dissection model was used to map two composite traits, stemwood volume growth decomposed into its stem height, stem diameter and stem form components for Euramerican poplar adult trees, and total lateral root length constituted by its average lateral root length and lateral root number components for Euphrates poplar seedlings. We found the pattern of how QTLs for different components contribute to phenotypic variation in composite traits. The detailed understanding of the genetic machineries of composite traits will not only help in the design of molecular breeding in plants and animals, but also shed light on the evolutionary processes of quantitative traits under natural selection.     

Symbiosis as a source of selectable epigenetic variation: taking the heat for the big guy

Evolutionary developmental biology is based on the principle that evolution arises from hereditable changes in development. Most of this new work has centred on changes in the regulatory components of the genome. However, recent studies (many of them documented in this volume) have shown that development also includes interactions between the organism and its environment. One area of interest concerns the importance of symbionts for the production of the normal range of phenotypes. Many, if not most, organisms have ‘outsourced’ some of their developmental signals to a set of symbionts that are expected to be acquired during development. Such intimate interactions between species are referred to as codevelopment, the production of a new individual through the coordinated interactions of several genotypically different species. Within the past 2 years, several research programmes have demonstrated that such codevelopmental schemes can be selected. We will focus on symbioses in coral reef cnidarians symbiosis, pea aphids and cactuses, wherein the symbiotic system provides thermotolerance for the composite organism.