Duality between time series and networks

Studying the interaction between a system's components and the temporal evolution of the system are two common ways to uncover and characterize its internal workings. Recently, several maps from a time series to a network have been proposed with the intent of using network metrics to characterize time series. Although these maps demonstrate that different time series result in networks with distinct topological properties, it remains unclear how these topological properties relate to the original time series. Here, we propose a map from a time series to a network with an approximate inverse operation, making it possible to use network statistics to characterize time series and time series statistics to characterize networks. As a proof of concept, we generate an ensemble of time series ranging from periodic to random and confirm that application of the proposed map retains much of the information encoded in the original time series (or networks) after application of the map (or its inverse). Our results suggest that network analysis can be used to distinguish different dynamic regimes in time series and, perhaps more importantly, time series analysis can provide a powerful set of tools that augment the traditional network analysis toolkit to quantify networks in new and useful ways.     

Sex-diagnosis of isolated Os coxae by discriminant functions

After methodical preparatory work on the selection of the metric characters and their technical definition, 16 variables were measured on every right hip bone in our standard series (Weisbach series). The discriminant functions performed on our standard series proved to be very sharply discriminant. The methodical foundation gained from the Weisbach series was applied to a control series (Tyrol series), whose sex had not been determined. The application of the discriminant analyses enabled a complete and plausible sex diagnosis to be made.     

Induction of heart failure: haemodynamic comparison of three different canine models

We compared three methods: arteriovenous anastomosis, doxorubicin administration, and combination of anastomosis and doxorubicin, with the intention of designing a simple, stable model of chronic heart failure. Twelve dogs were divided into three groups of four. One group received carotid-jugular anastomosis (Ana series), another group received anastomosis and doxorubicin injection (A/D series), and the last group received only doxorubicin (Dox series). Animals were followed for eight weeks. Fifteen different haemodynamic parameters were tracked and compared to baseline values. After eight weeks, diastolic pressure in the right atrium increased from 3.8+/-2.0 mmHg at baseline to 5.3+/-5.9 mmHg in the Ana series, to 6.3+/-3.3 mmHg in the Dox series and to 8.0+/-2.0 mmHg in the A/D series (P<0.05 A/D vs. baseline). Systolic pulmonary wedge pressure increased from 11.6+/-2.0 mmHg at baseline to 15.5+/-3.4 mmHg in the Ana series, 14.0+/-3.7 mmHg in the Dox series and 17.3+/-4.2 mmHg in the A/D series (P = NS vs. baseline). Left ventricular ejection fraction decreased from 53.9+/-10% at baseline to 36.1+/-5.6% in the Ana series (P<0.05 vs. baseline), 31.5+/-5.4% in the Dox series (P<0.05 vs. baseline) and 25.8+/-5.8% in the A/D series (P<0.001 vs. baseline, P<0.05 vs. Ana series and Dox series). In conclusion, eight weeks are not enough to produce stable heart failure using arteriovenous anastomosis alone. Doxorubicin administration alone produces a left ventricular failure. However, a combination of both of these interventions provides a more stable model of right-and left-sided heart failure.     

Synthesis and in vitro antitumor activity of asperphenamate derivatives as autophagy inducer

In an effort to improve the aqueous solubility and the antitumor activity of natural product asperphenamate, we have designed and synthesized three series of asperphenamate derivatives, including series I (simplifying molecular skeleton series), series II (introducing a hydroxyl group to A-phenyl ring series) and series III (disrupting molecular planarity series). All derivatives have displayed a significantly increased solubility compared with asperphenamate. Their growth inhibitory activities in vitro were screened by the standard MTT method in MCF-7, HeLa, and BEL-7402 cell lines. With the exception of the derivatives in series I, most of derivatives in series II and series III showed growth inhibitory activity. Among all derivatives, IM23b in series III showed the greatest potency in human breast cancer MCF-7 cells. The cellular potency of IM23b was approximately 1.5-fold more potent than that of cisplatin. The mechanism of cell death induced by IM23b in human breast cancer MCF-7 cells was further investigated. We concluded that the cell death was induced by autophagy instead of apoptosis or cell cycle arrest.     

Adaptation level effects in discrimination of flicker frequency

Pigeons accustomed to food reinforcement for responding in the presence of a 25-Hz flickering light were exposed to several sets of flicker-frequency stimuli arranged as increasing and decreasing series. In the first experiment, food was occasionally delivered for key pecks during 30-s periods of 25-Hz flicker appearing at the beginning, midway, and at the end of an ascending and descending series of nine frequencies, ranging from 13 to 37 Hz. These stimuli appeared for 15-s periods with no food available (extinction). Gradients of responding to flicker values in the ascending series differed from those in the descending series, showing displacements in peak responding toward the lower and higher frequency values, respectively. The same effects occurred when the sequence was changed so that a descending series was followed by an ascending series of frequencies. These effects are consonant with an adaptation level (AL) interpretation and were replicated in a second experiment in which durations of the extinction presentations were increased to 30s. In a final condition, only a descending series was presented and displacement of peak responding from 25 Hz to a higher frequency stimulus, 28 Hz, was observed.     

乙型、丙型流感病毒的长记忆ARFIMA模型

用时间序列模型来分析乙型、丙型这两种流感病毒,对乙流、丙流病毒DNA序列提供了一种新的时间序列模型,即CGR弧度序列。利用CGR坐标将乙流、丙流病毒DNA序列转换成CGR弧度序列,且引入长记忆ARFIMA模型去拟合这两类序列。发现随机找来的10条乙流序列,10条丙流序列都具有长相关性且拟合很好,并且还发现这两种病毒序列可以尝试用不同的ARFIMA模型ARFIMA(0,d,4)模型,ARFIMA(1,d,1)模型去识别。     

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     

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.     

Changes in evoked potentials during systematic exposure to a series of similar signals with variable intersignal intervals]

Series of clicks, standard by the number of stimuli and greatly varying by the length of interstimuli intervals in each series, were systematically presented to dogs without reinforcement. Evoked potentiale (EP) in the cortical auditory zone were recorded. It has been found that a typical U-shaped distribution of amplitude values of averaged EP is elaborated in the series in the course of repeated presentations; a maximal amplitude is observed in response to the first and last clicks, and a minimal, in the middle of the series. Such a regularity was previously found for the action of standard series with a constant interstimuli interval. It is assumed that an estimation may take place in the dog CNS of the number of signals used in a series, whose mechanism is not necessarily based on the time factor. The ability to estimate the number of signals in the series may be regarded as an elementary model of counting in the dogs' CNS.     

Human assessment of time intervals depending on the manner of their representation

On 42 subject three experimental series were carried out: in the first (12 persons) and second (24 persons) series the presented interval was limited by two short clicks, in the third series (6 persons)--by electrocutaneous stimuli. Duration of the stimuli was 1 ms. There were three regimes of work in the first and third series: the intervals successively increased from 100 to 500 ms with a step of 100 ms (1), decreased from 5000 to 100 ms (2) or varied in a random order (3). In the second series only the regime 3 was applied. In all series the method of temporal intervals reproduction was used. The means of the reproduction varied: in the second and third series the interval was reproduced by button pressing according to the presented duration: in the first series the end of the interval was marked by a short button push, and the beginning was the moment of the second stimulus presentation. With the first means a considerable overreproduction was observed of the presented duration at all intervals and all regimes. At the second and third series a phasic character of the reproduction duration was noted: up to 1000 ms the interval mostly was overestimated, over 2000 ms--it was significantly underestimated. It is suggested that as the estimation of the temporal interval implies some motor reaction, the afferent flow of signals from the active muscles can change the value of the reproduced duration. In the first series, the subjects probably do not take into account the time necessary for the realized signal perception.     

Testosterone propionate treatment of an XY gonadal dysgenetic chacma baboon

Behavioral studies of an XY gonadal dysgenetic chacma baboon prior to and during testosterone propionate treatment were carried out. The orchidectomized dysgenetic individual, two intact males, a castrate male, and two ovariectomized females were pair-tested with a group of eight ovariectomized stimulus females prior to and during their treatment with estradiol benzoate. Three test series were carried out. One series occurred prior to any treatment of the agonadal focal subject animals. During this series it was only the intact males who showed behavior change during their testing with the estrogen treated females. A second test series occurred after a month of daily testosterone propionate injections (1 mg/kg/day) had been given to the four agonadal subjects. During this test series the castrate male ejaculated once with one of the estrogen-treated females. All of the treated subjects showed increases in their frequency of yawning. Upon completion of this test series the androgen dosage was increased (2 mg/kg/day) and 2 weeks later a third test series was carried out. During this series the castrate male ejaculated with five of his eight estrogen-treated partners. The yawning of all the treated subjects continued. As had been the case in the second series the XY gonadal dysgenetic individual continued to behave as did the ovariectomized females. None of these animals showed any increase in any measure of male sexual behavior. This study establishes the fact that a genetic male primate deprived of in utero exposure to testicular hormones will go on to develop as a normal genetic female and will fail to exhibit increased levels of male sexual behavior during androgen treatment.     

Early classification of multivariate temporal observations by extraction of interpretable shapelets

ABSTRACT: BACKGROUND: Early classification of time series is beneficial for biomedical informatics problems suchincluding, but not limited to, disease change detection. Early classification can be oftremendous help by identifying the onset of a disease before it has time to fully take hold. Inaddition, extracting patterns from the original time series helps domain experts to gaininsights into the classification results. This problem has been studied recently using timeseries segments called shapelets. In this paper, we present a method, which we callMultivariate Shapelets Detection (MSD), that allows for early and patient-specificclassification of multivariate time series. The method extracts time series patterns, calledmultivariate shapelets, from all dimensions of the time series that distinctly manifest thetarget class locally. The time series were classified by searching for the earliest closestpatterns. RESULTS: The proposed early classification method for multivariate time series has been evaluated oneight gene expression datasets from viral infection and drug response studies in humans. Inour experiments, the MSD method outperformed the baseline methods, achieving highlyaccurate classification by using as little as 40%-64% of the time series. The obtained resultsprovide evidence that using conventional classification methods on short time series is notas accurate as using the proposed methods specialized for early classification. CONCLUSION: For the early classification task, we proposed a method called Multivariate ShapeletsDetection (MSD), which extracts patterns from all dimensions of the time series. Weshowed that the MSD method can classify the time series early by using as little as40%-64% of the time series' length.     

A Simple Approach for the Computation of Multiple Periodicities in Biological Time Series

We have described a simple approach for the analysis and isolation of multiple periodicities from a biological time series. For the estimation of the periodicities, we used simulated data and data from ongoing experiments in our laboratory. Two time series were simulated, one which consisted of only white noise and the other consisted white noise along with periodicities of 6, 11, 17 and 23 h, to demonstrate that our method can successfully isolate multiple patterns in a time series. Our method of analysis is objective, simple, flexible and adaptive since it distinctly delineates the individual contribution from an overlap of multiple periodicities. The key features of our method are: (i) identification of a reliable phase reference point, (ii) scanning the time series using a moving window in increments, (iii) use of Siegel's modification of Fisher's method to detect significant periodicit(y)ies in the time series. The use of window sizes of increasing length to examine the time series elegantly reduces noise while identifying periodicities that are otherwise not apparent. Finally, the periodogram can be smoothed in order to normalize the contribution by attendant frequency components within the waveform. A minimum critical value for relative contribution of various frequencies was calculated to delineate the periodicities that contributed significantly to the time series. We executed this method of time series analysis using MS Excel and C.     

金叶银杏半同胞子代无性系的叶色和色素含量变化及呈色机制分析

对4月份至11月份金叶银杏‘万年金'( Ginkgo biloba ‘Wannianjin')32个半同胞子代无性系与亲本的叶色差异进行比较;比较了不同色系叶片的色素含量和比值及叶色参数(L*、a*和b*)的变化,分析了叶色参数与叶片色素含量的相关性;并观察了不同色系的叶绿体超微结构。结果表明：32个半同胞子代无性系可被分为金黄、浅黄、草绿和蓝绿4个色系。随时间推移,草绿和蓝绿色系叶片的总叶绿素( Chl)、叶绿素a( Chla)、叶绿素b( Chlb)和类胡萝卜素( Car)含量均呈“双峰型”变化趋势,Car/Chl和Car/Chla比值的变幅均较小;而金黄和浅黄色系叶片的上述色素含量呈“升高—降低—升高”变化趋势,Car/Chl和Car/Chla比值总体呈“迅速下降—相对稳定—缓慢升高”的变化趋势。各色系叶片的上述色素含量在夏季均不同程度下降,Car/Chlb比值变化差异较大,且金黄和浅黄色系的各色素含量均低于草绿和蓝绿色系。随时间推移,金黄和浅黄色系叶片的L*、a*和b*值以及草绿和蓝绿色系叶片的L*和b*值均先降低后升高,后2个色系的a*值则先升高后下降;并且,前2个色系的L*和b*值总体上显著高于后2个色系,而a*值则总体上低于后2个色系。金黄色系的Chla和Chl含量与L*和a*值显著负相关,而其Car/Chl和Car/Chla比值则与L*、a*和b*值显著或极显著正相关;浅黄色系的Chlb含量与a*值显著负相关,其Car/Chla比值与L*和b*值以及Car/Chlb比值与a*值均显著正相关;草绿色系的Chla含量与L*值显著负相关,其Car/Chla比值与L*和b*值以及Car/Chlb比值与a*值均显著正相关;这3个色系叶片的其余指标间以及蓝绿色系叶片的各指标间均无显著相关性。观察结果显示：金黄和浅黄色系的叶绿体基粒片层发育不健全,基粒片层可见但排列较疏松,且无明显垛叠,分布范围小而稀疏;蓝绿和草绿色系叶绿体的基粒类囊体垛叠层数均较多,基粒片层发达且排列紧致、整齐,分布范围大而稠密。综合分析结果表明：‘万年金'4个色系半同胞子代无性系叶片的呈色差异和叶色变化由多种因素控制,其中,Car/Chl和Car/Chla比值高且叶绿体基粒片层发育不健全是叶片呈黄色的主要原因。     

A Simple Approach for the Computation of Multiple Periodicities in Biological Time Series

We have described a simple approach for the analysis and isolation of multiple periodicities from a biological time series. For the estimation of the periodicities, we used simulated data and data from ongoing experiments in our laboratory. Two time series were simulated, one which consisted of only white noise and the other consisted white noise along with periodicities of 6, 11, 17 and 23 h, to demonstrate that our method can successfully isolate multiple patterns in a time series. Our method of analysis is objective, simple, flexible and adaptive since it distinctly delineates the individual contribution from an overlap of multiple periodicities. The key features of our method are: (i) identification of a reliable phase reference point, (ii) scanning the time series using a moving window in increments, (iii) use of Siegel's modification of Fisher's method to detect significant periodicit(y)ies in the time series. The use of window sizes of increasing length to examine the time series elegantly reduces noise while identifying periodicities that are otherwise not apparent. Finally, the periodogram can be smoothed in order to normalize the contribution by attendant frequency components within the waveform. A minimum critical value for relative contribution of various frequencies was calculated to delineate the periodicities that contributed significantly to the time series. We executed this method of time series analysis using MS Excel and C.     

A Subsequent Fit of Time Series and Amplitude Histogram of Patch-Clamp Records Reveals Rate Constants up to 1 per Microsecond

Fast gating in time series of patch-clamp current demands powerful tools to reveal the rate constants of the adequate Hidden Markov model. Here, two approaches are presented to improve the temporal resolution of the direct fit of the time series. First, the prediction algorithm is extended to include intermediate currents between the nominal levels as caused by the anti-aliasing filter. This approach can reveal rate constants that are about 4 times higher than the corner frequency of the anti-aliasing filter. However, this approach is restricted to time series with very low noise. Second, the direct fit of the time series is combined with a beta fit, i.e., a fit of the deviations of the amplitude histogram from the Gaussian distribution. Since the “theoretical” amplitude histograms for higher-order Bessel filters cannot be calculated by analytical tools, they are generated from simulated time series. In a first approach, a simultaneous fit of the time series and of the Beta fit is tested. This simultaneous fit, however, inherits the drawbacks of both approaches, not the benefits. More successful is a subsequent fit: The fit of the time series yields a set of rate constants. The subsequent Beta fit uses the slow rate constants of the fit of the time series as fixed parameters and the optimization algorithm is restricted to the fast ones. The efficiency of this approach is illustrated by means of time series obtained from simulation and from the dominant K⁺ channel in Chara. This shows that temporal resolution can reach the microsecond range.     

Structure-affinity relationships of the affinity of 2-pyrazolyl adenosine analogues for the adenosine A2A receptor

The structure-affinity relationships of two novel 2-substituted adenosine series containing a substituted pyrazole attached at the N-1 or C-4 position for the adenosine (ADO) A2A receptor are described. Compounds in the 2-(N-1-pyrazolyl) adenosine series IV provided the highest affinity for the ADO A2A receptor as compared to the 2-(C-4-pyrazolyl) series V. The main structural differences between the two series point to the N-1 nitrogen of series IV imparting more favorable binding interactions with the receptor than those of series V.     

Analysis of cedar pollen time series: no evidence of low-dimensional chaotic behavior

Much of the current interest in pollen time series analysis is motivated by the possibility that pollen series arise from low-dimensional chaotic systems. If this is the case, short-range prediction using nonlinear modeling is justified and would produce high-quality forecasts that could be useful in providing pollen alerts to allergy sufferers. To date, contradictory reports about the characterization of the dynamics of pollen series can be found in the literature. Pollen series have been alternatively described as featuring and not featuring deterministic chaotic behavior. We showed that the choice of test for detection of deterministic chaos in pollen series is difficult because pollen series exhibit power spectra. This is a characteristic that is also produced by colored noise series, which mimic deterministic chaos in most tests. We proposed to apply the Ikeguchi–Aihara test to properly detect the presence of deterministic chaos in pollen series. We examined the dynamics of cedar (Cryptomeria japonica) hourly pollen series by means of the Ikeguchi–Aihara test and concluded that these pollen series cannot be described as low-dimensional deterministic chaos. Therefore, the application of low-dimensional chaotic deterministic models to the prediction of short-range pollen concentration will not result in high-accuracy pollen forecasts even though these models may provide useful forecasts for certain applications. We believe that our conclusion can be generalized to pollen series from other wind-pollinated plant species, as wind speed, the forcing parameter of the pollen emission and transport, is best described as a nondeterministic series that originates in the high dimensionality of the atmosphere.