Parametric construction of episode networks from pseudoperiodic time series based on mutual information

Recently, the construction of networks from time series data has gained widespread interest. In this paper, we develop this area further by introducing a network construction procedure for pseudoperiodic time series. We call such networks episode networks, in which an episode corresponds to a temporal interval of a time series, and which defines a node in the network. Our model includes a number of features which distinguish it from current methods. First, the proposed construction procedure is a parametric model which allows it to adapt to the characteristics of the data; the length of an episode being the parameter. As a direct consequence, networks of minimal size containing the maximal information about the time series can be obtained. In this paper, we provide an algorithm to determine the optimal value of this parameter. Second, we employ estimates of mutual information values to define the connectivity structure among the nodes in the network to exploit efficiently the nonlinearities in the time series. Finally, we apply our method to data from electroencephalogram (EEG) experiments and demonstrate that the constructed episode networks capture discriminative information from the underlying time series that may be useful for diagnostic purposes.     

Unbiased pattern detection in microarray data series

MOTIVATION: Following the advent of microarray technology in recent years, the challenge for biologists is to identify genes of interest from the thousands of genetic expression levels measured in each microarray experiment. In many cases the aim is to identify pattern in the data series generated by successive microarray measurements. RESULTS: Here we introduce a new method of detecting pattern in microarray data series which is independent of the nature of this pattern. Our approach provides a measure of the algorithmic compressibility of each data series. A series which is significantly compressible is much more likely to result from simple underlying mechanisms than series which are incompressible. Accordingly, the gene associated with a compressible series is more likely to be biologically significant. We test our method on microarray time series of yeast cell cycle and show that it blindly selects genes exhibiting the expected cyclic behaviour as well as detecting other forms of pattern. Our results successfully predict two independent non-microarray experimental studies.     

Competition between plant populations with different rooting depths II. Pot experiments

Summary In a previous paper in this series a model was proposed lor the competition between plant populations with different rooting depths. This model predicts that in mixtures of plant populations with different rooting depths the Relative Yield Total will exceed unity. Secondly it predicts that in these mixtures the relative crowding coefficient of the deep rooting population with respect to the shallow rooting one will decrease with increasing plant frequency. Two competition experiments in deep pots are carried out to test these predictions. In the first experiment a comparison is made between a series in which nutrients limited plant growth severely and a series in which nutrients were applied in a quantity that allowed high productivity. In the nutrient poor series the Relative Yield Total exceeded unity by about twenty per cent, while in the nutrient rich series only a small deviation from one was observed. The second experiment was divided into a series of deep pots in which different rooting depths were possible and a series of shallow pots in which the two species were forced to share the same space. In the series of shallow pots the relative crowding coefficient of the two species was found to be independent of plant frequency. In the series of deep pots the relative corowding coefficient of the two species with respect to each other did decrease significantly with increasing frequency.The observed frequency-dependence for the shallow rooting species could be explained by an extension of the theory presented previously. In the spacing series used in the same experiment a decrease of the shoot to root ratio with increasing plant density was observed. Furthermore, in the replacement series the shoot to root ratio in mixture was found to be lower than in monoculture. The consequences of these phenomena for the estimation of the relative crowding coefficient and the Relative Yield Total on the basis of shoot weights are discussed. However, it is argued that the fact that shoot to root ratios change with plant frequency does not provide an alternative explanation for the frequency-dependence observed.Grassland Research Group Publication No. 33     

Energy-Based Wavelet De-Noising of Hydrologic Time Series

De-noising is a substantial issue in hydrologic time series analysis, but it is a difficult task due to the defect of methods. In this paper an energy-based wavelet de-noising method was proposed. It is to remove noise by comparing energy distribution of series with the background energy distribution, which is established from Monte-Carlo test. Differing from wavelet threshold de-noising (WTD) method with the basis of wavelet coefficient thresholding, the proposed method is based on energy distribution of series. It can distinguish noise from deterministic components in series, and uncertainty of de-noising result can be quantitatively estimated using proper confidence interval, but WTD method cannot do this. Analysis of both synthetic and observed series verified the comparable power of the proposed method and WTD, but de-noising process by the former is more easily operable. The results also indicate the influences of three key factors (wavelet choice, decomposition level choice and noise content) on wavelet de-noising. Wavelet should be carefully chosen when using the proposed method. The suitable decomposition level for wavelet de-noising should correspond to series'' deterministic sub-signal which has the smallest temporal scale. If too much noise is included in a series, accurate de-noising result cannot be obtained by the proposed method or WTD, but the series would show pure random but not autocorrelation characters, so de-noising is no longer needed.     

Three-dimensional reconstruction of chromatin fibers

We have obtained tilt series of thin sections of chromatin fibers embedded in araldite-epon and stained with uranyl acetate. The tilt series contain between 12 and 18 micrographs, spanning tilt ranges between 84 and 117 degrees. Reconstructions in three dimensions have been obtained by filtered back-projection from each tilt series. The reconstructions have been low-pass filtered in order to reduce the amount of noise. In the reconstructions it is possible to approximately localize the nucleosomes. In several regions they show a clear zigzag arrangement, but in other regions it is difficult to determine the sequence of the nucleosomes. In any case there is no clear indication of a solenoidal arrangement. We discuss the rules which may give rise to a 3-D arrangement of the nucleosomal zigzag.     

Scalar modeling and analysis of a 3D biochemical reaction model

For many systems it is advantageous if analysis and modeling can be accomplished from a scalar time series because this greatly facilitates the experimental setup. Moreover, in real-life systems it is hardly true that all the state variables are available for analysis and modeling. Since the late 1980s, techniques have been put forward for building mathematical models from a scalar time series. One of the objectives of this paper is to verify if it is possible to obtain global non-linear models (non-linear differential equations) from scalar time series. Such data are obtained using a model of biochemical reaction with aperiodic (chaotic) oscillations as recently observed in the case of a glycolytic reaction (Nielsen, K., Sorensen, P.G., Hynne, F., 1997. Chaos in glycolysis. J Theor. Biol. 186, 303-306.). The main objective, however, is to investigate which state variable is more convenient for the task in practice. It is shown that observability indices seem to quantify quite well which variable should be preferred as the observable. The validity of the results are established performing rigorous topological analysis on the original system and the obtained models. The influence of noise, always present in experimental time series, on the dynamics underlying such a system is also investigated.     

Three-Dimensional Reconstruction of Chromatin Fibers

Abstract

We have obtained tilt series of thin sections of chromatin fibers embedded in araldite-epon and stained with uranyl acetate. The tilt series contain between 12 and 18 micrographs, spanning tilt ranges between 84 and 117 degrees. Reconstructions in three dimensions have been obtained by filtered back-projection from each tilt series. The reconstructions have been low-pass filtered in order to reduce the amount of noise. In the reconstructions it is possible to approximately localize the nucleosomes. In several regions they show a clear zigzag arrangement, but in other regions it is difficult to determine the sequence of the nucleosomes. In any case there is no clear indication of a solenoidal arrangement. We discuss the rules which may give rise to a 3-D arrangement of the nucleosomal zigzag.     

The basic property of biomembranes

In order to explain the experimentally obtained results with biomembranes it has been assumed, that the diameter of all vesicles, defined by a lipid bilayer, form a perfect crystal. Later on it appeared that biomembranes are liquid crystals. Nevertheless already with biomembranes as crystals it was possible to calculate the diameters of all existing vesicles. As shown in the present paper, the results with liquid crystals were identical to those with a perfect crystal-model. Here I demonstrate that the geometric progression of the diameters of vesicles of biomembranes is based on the entropy of the lipids and it is shown that the diameters of biomembranes fit four geometric series. The surface areas of these series of biomembranes can be approximated by the two geometric series published previously. The experiments and the theoretical studies on which this work is based have been carried out at the Netherlands Cancer Institute, Amsterdam, The Netherlands.     

A search for a paternal-age effect upon cases of 47, +21 in which the extra chromosome is of paternal origin

If there is a paternal-age effect for 47, +21, it would appear most likely to be present primarily, if not exclusively, in cases in which the extra chromosome is of paternal origin. To search for such an effect, data were reviewed from seven series reporting at least four cases of 47, +21 of paternal origin. The mean of the paternal age-maternal-age difference of such cases (dp) in each series was compared with the mean of the paternal-age differences of cases in the same series that were of maternal origin (dm). If the difference between these (dp - dm or delta) is greater than zero, then this would imply a positive paternal-age effect among cases of paternal origin, at least compared to those of maternal origin. In the seven series, the values of delta ranged from -2.2 years to +3.4 years, and there was no evidence in these comparisons for any consistent trend. A second analysis controlled for any effect of maternal-age variation upon this difference. Each case of paternal origin was matched with a case of maternal origin in the same series that was of the same maternal age. Of 60 cases of paternal origin, exact matches were found for 38. In these 38, the mean value of the difference in parental ages, dp - dm or delta, was negative, about -1.1 (+/- 5.1 years). The difference was highest for the nine cases of paternal origin in which the extra chromosome resulted from presumptive second-division non-disjunction, -1.8 (+/- 3.8 years).(ABSTRACT TRUNCATED AT 250 WORDS)     

Transient distributions arising from initially sharp boundaries in the ultracentrifuge

An infinite series solution to the Mason-Weaver equation is presented for the case in which a synthetic boundary is formed originally between solution and solvent. Digital computations based on this series, and confirmed independently, have been made for a range of parameters. For given conditions, the maximum rate of change of concentration at the meniscus and the time at which it occurs can be easily estimated by means of the curves presented. In equilibrium experiments which commence with formation of a sharp boundary, this enables the fringes to be identified with certainty.     

Relationship between multidrug resistance,hypersensitivity to resistance modifiers and cell volume in Chinese hamster ovary cells.

We have previously shown that very high levels of hypersensitivity to several resistance modifiers are correlated with increasing multidrug resistance in a series of Chinese hamster ovary cell lines. We have now selected a new member of the series which is an exception to this correlation in that although it is almost twice as multidrug resistant as the cell line from which it was derived, it shows much less hypersensitivity to resistance modifiers. Level of resistance modifier hypersensitivity correlated with the level of reduction of verapamil accumulation in these cells, and with the density of P-glycoprotein, but since the selection of this cell line has involved a doubling of cell volume, it was not correlated with total amount of P-glycoprotein.     

论丹霞地貌区生态演替特征及其科学价值

论述了丹霞地貌区生态演替的特征及其科学价值.认为植被演替由于时间漫长、过程复杂而对其研究具极大的难度,时空互代成为演替研究的重要手段,而这需要有完整的空间序列.丹霞地貌区存在着完整的原生演替与次生演替系列.典型丹霞地貌的山顶为原生演替的矮灌木林和乔木林,周围斜坡仍然受季节性降水侵蚀、风化、重力崩塌等作用,原生演替不断从裸露的岩石开始,故形成原生演替早期的苔藓、草本群落,随着岩石的进一步风化和苔藓、地衣等植物的作用,土壤层增厚,将原生演替继续往前推进.特殊的地质地貌过程使之不断有新的崩塌,从裸露的岩石开始的新的原生演替,如此形成不同时间系列的原生演替阶段.丹霞地貌区也存在着完整的次生演替系列,同时存在演替先锋林、演替过渡林和演替基本稳定林.这两个演替系列提供了一个非常难得的理想场所,使得生态学工作者在一个地点就可以观察到一个完整的植被演替系列.其研究可为该区域植被的经营管理和保护措施提供必要的依据.作为生态恢复参照系,对区域的植被生态恢复具有重要的指导意义.＃     

Artificial neural network learning of nonstationary behavior in time series

We refine and complement a previously-proposed artificial neural network method for learning hidden signals forcing nonstationary behavior in time series. The method adds an extra input unit to the network and feeds it with the proposed profile for the unknown perturbing signal. The correct time evolution of this new input parameter is learned simultaneously with the intrinsic stationary dynamics underlying the series, which is accomplished by minimizing a suitably-defined error function for the training process. We incorporate here the use of validation data, held out from the training set, to accurately determine the optimal value of a hyperparameter required by the method. Furthermore, we evaluate this algorithm in a controlled situation and show that it outperforms other existing methods in the literature. Finally, we discuss a preliminary application to the real-world sunspot time series and link the obtained hidden perturbing signal to the secular evolution of the solar magnetic field.     

Morphological phase-contrast cinematographic studies on the behavior of bone marrow cells in vitro. X. Myeloblasts and monoblasts]

The myeloblast is nearly of the same size as the lymphozyte and has the same nucleus cytoplasma ratio of 0.7 but differs from it in its morphology, its high frequency of multiplication, and by its kinetic behaviour. By phase contrast observation the transformation of the myeloblast into the promyelocyte has been seen several times. The myeloblast like the lymphocyte is able to move although at a much slower speed. By locomotion the myeloblast, and likewise the lymphocyte can move between blood and bone marrow. Of the granulocytopoietic series only the promyelocyte and the myelocyte with their nuclear cytoplasm relation of 0.3 are found in the bone marrow. The monoblast but is about twice its size, and moves less often. Apart from its transformation into promonocyte, monocyte and histiocyte, the monoblast may evalue in another way: it grows into a cell of doubled size with the same nucleus cytoplasm ratio 0.7 in whose cytoplasm are seen a lot of big granules. The cell may now be characterized as a tissue macrophage or mastcell. In consequence a frequently multiplying basophilic cell with a coarse nuclear structure and nucleoli, grows from a diameter of 6.5 to one of 13.0 mum without marked morphologic change apart from becoming alpha-NA-Esterase positive and acquiring big lysosomes. When this haemocytoblast is small (K 1/4 to K 1/2), it can be triggered into the granulocytopoietic series, when it is bigger (K 1/2 to K1) into the monocytopoietic series, or in the size K1 to K2 by erythropoietin into the erythropoietic series. If no triggering takes place, the cell degenerates after having granulated. The lymphopoietic system is not connected to this system of stem cells committed to the granulocytopoietic, the monocytopoietic and the erythropoietic series. Therefore we postulate a dual haematopoietic system. In acute leukemias the spread of size of cells and nuclei is wider and kinetically active stem cells are rarer. Only leukemic promyelocytes are in locomotion vividly, in contrast to the normal ones. In leukemic myeloblasts there are fewer mitoses than in normal ones, but in leukemic promyelocytes and monoblasts the mitotic frequency is not reduced.     

Allele and locus classification in electrophoretic population studies

The electrophoretic separation of protein variants having slightly different mobilities is a basic tool of biochemical population genetics. In certain situations it is difficult to determine how to classify the variants as alleles of a number of genetic loci, that is, as variant subsets within each of which the Mendelian laws hold. In this article, we develop and analyze a series of algorithms for solving various versions and generalizations of this problem of optimal classification.     

Predicting Physical Time Series Using Dynamic Ridge Polynomial Neural Networks

Forecasting naturally occurring phenomena is a common problem in many domains of science, and this has been addressed and investigated by many scientists. The importance of time series prediction stems from the fact that it has wide range of applications, including control systems, engineering processes, environmental systems and economics. From the knowledge of some aspects of the previous behaviour of the system, the aim of the prediction process is to determine or predict its future behaviour. In this paper, we consider a novel application of a higher order polynomial neural network architecture called Dynamic Ridge Polynomial Neural Network that combines the properties of higher order and recurrent neural networks for the prediction of physical time series. In this study, four types of signals have been used, which are; The Lorenz attractor, mean value of the AE index, sunspot number, and heat wave temperature. The simulation results showed good improvements in terms of the signal to noise ratio in comparison to a number of higher order and feedforward neural networks in comparison to the benchmarked techniques.     

Algerian ivy dermatitis; a California disease

A hitherto unrecognized cause of contact dermatitis in California is the widely cultivated plant known as Algerian ivy. This plant, which grows in California (and its close relative, English ivy) causes a dermatitis which is similar to although milder than that caused by poison oak. Dermatitis from this cause occurs most frequently when persons who have become sensitive to it by previous contact trim the plant back in the spring after its seasonal spurt of growth. For persons whose occupations require repeated contact with the plant, dermatitis from this cause is an occupational hazard. Dermatitis from this plant is easily diagnosed by means of a simple patch test. In a series of 12 cases the only effective treatment was with corticosteroid agents.     

ALGERIAN IVY DERMATITIS—A California Disease

A hitherto unrecognized cause of contact dermatitis in California is the widely cultivated plant known as Algerian ivy. This plant, which grows in California (and its close relative, English ivy) causes a dermatitis which is similar to although milder than that caused by poison oak. Dermatitis from this cause occurs most frequently when persons who have become sensitive to it by previous contact trim the plant back in the spring after its seasonal spurt of growth. For persons whose occupations require repeated contact with the plant, dermatitis from this cause is an occupational hazard. Dermatitis from this plant is easily diagnosed by means of a simple patch test.In a series of 12 cases the only effective treatment was with corticosteroid agents.