时间序列的相似性测度

时间序列（time series）是指按时间顺序排列的观测值集合,在生物信息学研究领域中,DNA序列和基因表达数据都可以视为时间序列数据。时间序列分析中很重要的环节就是刻划两个时间序列或者时间子序列的相似性,用于序列比对等。时间序列的相似性测度是时间序列研究中的基础和重点,直接影响查询、聚类等后续计算的效率和精度,在高通量基因芯片数据分析、基因网络构建等研究中,具有重要的应用,目前已引起了众多研究人员的关注,在欧氏距离的基础上进行了大量的研究,本文综述了基于欧式距离和时间弯曲的时间序列相似性测度及其相关领域的研究进展,可作为进一步研究的参考。     

Effects of extra food on population fluctuation patterns of the muroid rodent Calomys venustus

Population dynamics in the South American muroid rodent Calomys venustus are described from a 14‐year continuous data series, using the auto‐regressive integrated moving average (arima ) model. Population responses to experimental food addition were analysed in two experimental areas, over two periods, using intervention analysis. There was no consistent evidence that food quantity leads to peaks in population density. Significant increases were related to densities of transients and juvenile individuals.     

基于DTW距离的DNA序列相似性分析

在DNA序列相似性的研究中,通常采用的动态规划算法对空位罚分函数缺乏理论依据而带有主观性,从而取得不同的结果,本文提出了一种基于DTW（Dynamic Time Warping,动态时间弯曲）距离的DNA序列相似性度量方法可以解决这一问题．通过DNA序列的图形表示把DNA序列转化为时间序列,然后计算DTW距离来度量序列相似度以表征DNA序列属性,得到能够比较DNA序列相似性度量方法,并用这个方法比较分析了七种东亚钳蝎神经毒素（Buthusmartensi Karsch neurotoxin）基因序列的相似性,验证了该度量方法的有效性和准确性．     

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called `wavelet transform microscope' reveals a characteristic scale of 100-200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called wavelet-based multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1, 2].     

Effects of weather and climate on the dynamics of animal population time series

Weather is one of the most basic factors impacting animal populations, but the typical strength of such impacts on population dynamics is unknown. We incorporate weather and climate index data into analysis of 492 time series of mammals, birds and insects from the global population dynamics database. A conundrum is that a multitude of weather data may a priori be considered potentially important and hence present a risk of statistical over-fitting. We find that model selection or averaging alone could spuriously indicate that weather provides strong improvements to short-term population prediction accuracy. However, a block randomization test reveals that most improvements result from over-fitting. Weather and climate variables do, in general, improve predictions, but improvements were barely detectable despite the large number of datasets considered. Climate indices such as North Atlantic Oscillation are not better predictors of population change than local weather variables. Insect time series are typically less predictable than bird or mammal time series, although all taxonomic classes display low predictability. Our results are in line with the view that population dynamics is often too complex to allow resolving mechanisms from time series, but we argue that time series analysis can still be useful for estimating net environmental effects.     

Computer Simulation of Liquid Methanol II. System Size Effects

Abstract

A series of molecular dynamics simulations of liquid methanol has been carried out on a supernode transputer array. Four system sizes from 125 to 512 molecules have been considered, in order to study the effect of system size on the calculated structural, orientational and dynamic properties. The dielectric constant and the dielectric relaxation time are compared with experimental data.     

Disorders of the Menstrual Cycle in Elite Female Ice Hockey Players and Figure Skaters

The purpose of this study was to assess and compare the incidence of delayed menarche and menstrual dysfunction among elite ice hockey players and figure skaters. Forty-three ice hockey players (23.5 ± 4.8 years, 68.2 ± 1.2 kg, 1.68 ± 0.01 m) and 39 figure skaters (17.5 ± 3.4 years, 53.7 ± 5.8 kg, 1.64 ± 0.05 m) completed a self-administered questionnaire on their menstrual status and history, training regimens and lifestyle. Age at menarche did not differ significantly between ice hockey players (13.3 ± 1.3 years) and figure skaters (13.7 ± 1.4 years). Menarche was unrelated to nationality, vigorous training premenarche or age at which the athlete began her sport, but was correlated with the age at menarche of the athletes’ mothers (r = 0.39, p < 0.05). Hormonal contraceptives were used by 35% of ice hockey players and 15% of the figure skaters. Amenorrhea and oligomenorrhea were experienced by 7.1% and 38.7% of postmenarcheal, ice hockey players and figure skaters respectively not using hormonal contraceptives. Menstrual dysfunction was associated with both age and age at menarche in the ice hockey players only. Training factors, and psychological pressure were perceived by the athletes to contribute to menstrual dysfunction. A greater training volume, younger age at commencing sport, lower body mass, greater subjective body image pressure and younger biological and gynaecological age were reported among the figure skaters, and were proposed to explain the higher incidence of menstrual dysfunction among the figure skaters compared with the ice hockey players. Figure skaters appear at increased risk of amenorrhea and oligomenorrhea compared with ice hockey players, which may be linked to training and physical characteristics of the sports.     

Ciliary Beating Compartmentalizes Cerebrospinal Fluid Flow in the Brain and Regulates Ventricular Development

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Fractal rigidity by enhanced sympatho-vagal antagonism in heartbeat interval dynamics elicited by central application of corticotropin-releasing factor in mice

The dynamics of heartbeat interval fluctuations were studied in awake unrestrained mice following intracerebroventricular application of the neuropeptide corticotropin-releasing factor (CRF). The cardiac time series derived from telemetric ECG monitoring were analyzed by non-parametric techniques of nonlinear signal processing: delay-vector variance (DVV) analysis, higher-order variability (HOV) analysis, empirical mode decomposition (EMD), multiscale embedding-space decomposition (MESD), multiexponent multifractal (MEMF) analysis. The analyses support the conjecture that cardiac dynamics of normal control mice has both deterministic and stochastic elements, is nonstationary, nonlinear, and exerts multifractal properties. Central application of CRF results in bradycardia and increased variability of the beat-to-beat fluctuations. The altered dynamical properties elicited by CRF reflect a significant loss of intrinsic structural complexity of cardiac control which is due to central neuroautonomic hyperexcitation, i.e., enhanced sympatho-vagal antagonism. The change in dynamical complexity is characterized by an effect referred to as fractal rigidity, leading to a significant impairment of adaptability to extrinsic challenges in a fluctuating environment. The impact of dynamical neurocardiopathy as a major precipiting factor for the propensity of cardiac arrhythmias or sudden cardiac death by unchecked central CRF release in significant acute life events in man is critically discussed.     

Estimating Competition in Cladocerans Using Data on Dynamics of Clutch Size and Population Density

Negative correlations between clutch size and population density are proposed to be considered as indices of intra- and interspecific competition in cladocerans if they are revealed while analyzing population dynamics and clutch size and time lags are taken into account. The proper correlation analysis of summer populations of Diaphanosoma brachyurum, Bosmina coregoni, Daphnia cucullata and D. galeata from mesotrophic Lake Glubokoye (Moscow Region) in 1975, 1978, and 1979 indicates the important role of competition of both types for the community studied. High niche overlap in food and space in the four populations was also observed.     

Analysis on Jinghe watershed vegetation dynamics and evaluation on its relation with precipitation

Vegetation degradation is one of the key subjects in the study of global environmental changes, and the Normalized Difference Vegetation Index (NDVI) is generally recognized as a good indicator of terrestrial vegetation productivity and growth status. To evaluate the vegetation dynamic changes in the Jinghe watershed on Loess plateau from 1982 to 2003, major methods of change slope, principal component analysis and correlation analysis were employed with 8 km resolution NOAA-NDVI time series data. Based on these analyses, the relationship between precipitation and NDVI was discussed. Results show that there has been little change in both amplitude and variety of NDVI during the past 22 years. Vegetation in the upper stream areas, typically the watershed marginal mountain areas, changes significantly. A trend analysis shows that the similar finding on vegetation dynamics in different areas tends to be induced by climate changes and human land use transformation. A standardized principal component analysis indicates that the first two components, PC1 and PC2, are closely related to vegetation and climate changes, while PC3 and PC4 are connected with floodwater in flooding seasons, and PC5 and PC6 reflect the effects of human activities. Finally, the correlation analysis shows that there is a close positive relationship in this region between NDVI and precipitation. The rainfall sensitivity threshold reaches 550 mm or even higher.     

Analysis on Jinghe watershed vegetation dynamics and evaluation on its relation with precipitation

Vegetation degradation is one of the key subjects in the study of global environmental changes, and the Normalized Difference Vegetation Index (NDVI) is generally recognized as a good indicator of terrestrial vegetation productivity and growth status. To evaluate the vegetation dynamic changes in the Jinghe watershed on Loess plateau from 1982 to 2003, major methods of change slope, principal component analysis and correlation analysis were employed with 8 km resolution NOAA-NDVI time series data. Based on these analyses, the relationship between precipitation and NDVI was discussed. Results show that there has been little change in both amplitude and variety of NDVI during the past 22 years. Vegetation in the upper stream areas, typically the watershed marginal mountain areas, changes significantly. A trend analysis shows that the similar finding on vegetation dynamics in different areas tends to be induced by climate changes and human land use transformation. A standardized principal component analysis indicates that the first two components, PC1 and PC2, are closely related to vegetation and climate changes, while PC3 and PC4 are connected with floodwater in flooding seasons, and PC5 and PC6 reflect the effects of human activities. Finally, the correlation analysis shows that there is a close positive relationship in this region between NDVI and precipitation. The rainfall sensitivity threshold reaches 550 mm or even higher.     

Non-linear, non-invasive method for seizure anticipation in focal epilepsy

In this paper we discuss an approach, using methods of non-linear time series analysis applied to scalp electrode recordings, which is able to distinguish between epochs temporally distant from and just prior to, the onset of a seizure in patients with temporal lobe epilepsy. The method involves a comparison of recordings taken from electrodes adjacent to and remote from the site of ictal onset. In particular, we define a non-linear quantity which we call 'marginal predictability'. This quantity is computed using data from remote and from adjacent electrodes. We find that the difference between the marginal predictabilities computed for the remote and adjacent electrodes decreases several tens of minutes prior to seizure onset, compared to its value interictally.     

Spectral analysis of unequally spaced sampled time series

Abstract

The diurnal excretion patterns of several electrolytes and urea were studied in 5 freely moving rats on an elemental diet (Vivonex) administered either orally or as a continuous intragastric feeding; the lights were on from 07.00–19.00 h and off from 19.00–07.00 h. During continuous feeding the diurnal rhythms persisted, although the amplitude was lower than during oral feeding. The maximum excretion rates of potassium, phosphate and urea all coincided under both feeding regimens. The time of the maximum calcium excretion rate coincided with that of sodium during oral feeding but not during continuous feeding. During continuous feeding the maximum calcium excretion rate shifted from 04.00 to 10.00 h. The diurnal excretion of magnesium during continuous feeding was abolished, possibly as a result of the low calcium intake. From this study it can be concluded that duringcontinuous intragastric feeding all of the studied excretion patterns persist, with the exception of magnesium, which indicates that these rhythms are not merely the result of the intermittent intake of food and minerals.     

Symbolic dynamics for identifying similarity between rhythms of ecological time series

Explaining the associations between animal populations or between population and environmental signals is an important challenge. The time series that quantify animal populations are often complex, nonlinear, noisy and non‐stationary. These characteristics may make it inappropriate to use traditional techniques when analysing these time series and their mutual dependencies. Here I propose to use symbolic dynamics and techniques from Information Theory to evaluate the degree of dynamic cohesion between time series fluctuations. The main idea is to check whether two (or more) signals tend to oscillate simultaneously, rising and falling together with the same rhythm. Based on synthetic and real time series, I demonstrate that this method is robust to the presence of noise and to the short length of the analysed time series and gives relevant information about the weak relationships between different series. Furthermore, this method appears as simple as classical cross‐correlation and outperforms it in the analysed examples.     

城市化对区域生态足迹供需的影响

基于1994-2003年吉林省生态足迹时间序列,建立了城市化水平与生态足迹、生态盈亏、生态足迹强度的关系模型.结果表明:吉林省生态足迹、生态盈亏、生态足迹强度与城市化率呈显著相关;生态足迹随城市化的发展由1994年的每人1.59 hm2增至2003年的每人2.23 hm2,主要受城市化率和第三产业比例的影响;建筑用地、草地和化石燃料用地生态足迹的变化较显著,建筑用地生态足迹变化的驱动因素以人均GDP和第三产业比例为主,草地和化石燃料用地生态足迹主要受居民消费水平的影响;源于居民消费水平的驱动作用,吉林省生态赤字渐趋恶化,从1994年的每人0.319 hm2增至2003年的每人0.923 hm2;草地和化石燃料用地生态盈亏的变化最显著;在经济结构和消费结构优化的驱动下,研究期间生态足迹强度从每万元4.14 hm2降至2.35 hm2,而且仍具有较大的降低空间.通过调整经济结构和消费结构,吉林省可以消除生态赤字、实现自然资源的供需平衡.