Quantitative PCR deconstruction of discrepancies between results reported by different hybridization platforms.

Differences in hybridization platforms used in gene array analysis experiments can lead to significant differences in hybridization results. In this study we used quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to investigate discrepant results between the National Institute of Environmental Health Sciences cDNA and Affymetrix oligo platforms used to evaluate hepatic gene expression changes in rats exposed to methapyrilene. Caldesmon cDNA platform hybridization results showed decreases in gene expression levels for the high-dose methapyrilene 7-day pooled samples compared with their controls. By contrast, the Affymetrix oligonucleotide platform showed increases in expression levels for these samples. Quantitative gene expression measurements provide an explanation for the discrepancies observed for these samples. In the case of caldesmon, there is a 74-base sequence in the cDNA clone that is absent in the Affymetrix sequence. The amplicon based on the cDNA clone shows > 100-fold suppression relative to the day 7 high-dose methapyrilene-pooled control. These data demonstrate the importance of using a "gold standard," such as qRT-PCR to confirm key hybridization results as well as to understand the sources of discrepancies resulting from different hybridization platforms

Detection of synchronization from univariate data using wavelet transform

A method is proposed for detecting from univariate data the presence of synchronization of a self-sustained oscillator by external driving with varying frequency. The method is based on the analysis of difference between the oscillator instantaneous phases calculated using continuous wavelet transform at time moments shifted by a certain constant value relative to each other. We apply our method to a driven asymmetric van der Pol oscillator, experimental data from a driven electronic oscillator with delayed feedback and human heartbeat time series. In the latest case, the analysis of the heart rate variability data reveals synchronous regimes between the respiration and slow oscillations in blood pressure.Comment: 10 pages, 9 figure

On the Feasibility of Malware Authorship Attribution

There are many occasions in which the security community is interested to discover the authorship of malware binaries, either for digital forensics analysis of malware corpora or for thwarting live threats of malware invasion. Such a discovery of authorship might be possible due to stylistic features inherent to software codes written by human programmers. Existing studies of authorship attribution of general purpose software mainly focus on source code, which is typically based on the style of programs and environment. However, those features critically depend on the availability of the program source code, which is usually not the case when dealing with malware binaries. Such program binaries often do not retain many semantic or stylistic features due to the compilation process. Therefore, authorship attribution in the domain of malware binaries based on features and styles that will survive the compilation process is challenging. This paper provides the state of the art in this literature. Further, we analyze the features involved in those techniques. By using a case study, we identify features that can survive the compilation process. Finally, we analyze existing works on binary authorship attribution and study their applicability to real malware binaries.Comment: FPS 201

Lag time and parameter mismatches in synchronization of unidirectionally coupled chaotic external cavity semiconductor lasers

We report an analysis of synchronization between two unidirectionally coupled chaotic external cavity master/slave semiconductor lasers with two characteristic delay times, where the delay time in the coupling is different from the delay time in the coupled systems themselves. We demonstrate for the first time that parameter mismatches in photon decay rates for the master and slave lasers can explain the experimental observation that the lag time is equal to the coupling delay time.Comment: LaTex, 5 pages, submitted to PRE(R

Generalized Chaotic Synchronizationin Coupled Ginzburg-Landau Equations

Generalized synchronization is analyzed in unidirectionally coupled oscillatory systems exhibiting spatiotemporal chaotic behavior described by Ginzburg-Landau equations. Several types of coupling betweenthe systems are analyzed. The largest spatial Lyapunov exponent is proposed as a new characteristic of the state of a distributed system, and its calculation is described for a distributed oscillatory system. Partial generalized synchronization is introduced as a new type of chaotic synchronization in spatially nonuniform distributed systems. The physical mechanisms responsible for the onset of generalized chaotic synchronization in spatially distributed oscillatory systems are elucidated. It is shown that the onset of generalized chaotic synchronization is described by a modified Ginzburg-Landau equation with additional dissipation irrespective of the type of coupling. The effect of noise on the onset of a generalized synchronization regime in coupled distributed systems is analyzed.Comment: 12 page

Conspicuous male coloration impairs survival against avian predators in Aegean wall lizards, Podarcis erhardii.

This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/ece3.1650Animal coloration is strikingly diverse in nature. Within-species color variation can arise through local adaptation for camouflage, sexual dimorphism and conspicuous sexual signals, which often have conflicting effects on survival. Here, we tested whether color variation between two island populations of Aegean wall lizards (Podarcis erhardii) is due to sexual dimorphism and differential survival of individuals varying in appearance. On both islands, we measured attack rates by wild avian predators on clay models matching the coloration of real male and female P. erhardii from each island population, modeled to avian predator vision. Avian predator attack rates differed among model treatments, although only on one island. Male-colored models, which were more conspicuous against their experimental backgrounds to avian predators, were accordingly detected and attacked more frequently by birds than less conspicuous female-colored models. This suggests that female coloration has evolved primarily under selection for camouflage, whereas sexually competing males exhibit costly conspicuous coloration. Unexpectedly, there was no difference in avian attack frequency between local and non-local model types. This may have arisen if the models did not resemble lizard coloration with sufficient precision, or if real lizards behaviorally choose backgrounds that improve camouflage. Overall, these results show that sexually dimorphic coloration can affect the risk of predator attacks, indicating that color variation within a species can be caused by interactions between natural and sexual selection. However, more work is needed to determine how these findings depend on the island environment that each population inhabits.This work was supported by a Biotechnology and Biological Sciences Research Council studentship, Magdalene College, Cambridge and the British Herpetological Society (K.L.A.M), and a Biotechnology and Biological Sciences Research Council and David Philips Research Fellowship (grant number BB/G022887/1) to M.S

Synchronization of chaotic oscillator time scales

This paper deals with the chaotic oscillator synchronization. A new approach to detect the synchronized behaviour of chaotic oscillators has been proposed. This approach is based on the analysis of different time scales in the time series generated by the coupled chaotic oscillators. It has been shown that complete synchronization, phase synchronization, lag synchronization and generalized synchronization are the particular cases of the synchronized behavior called as "time--scale synchronization". The quantitative measure of chaotic oscillator synchronous behavior has been proposed. This approach has been applied for the coupled Rossler systems.Comment: 29 pages, 11 figures, published in JETP. 100, 4 (2005) 784-79

Periodicity Manifestations in the Turbulent Regime of Globally Coupled Map Lattice

We revisit the globally coupled map lattice (GCML). We show that in the so called turbulent regime various periodic cluster attractor states are formed even though the coupling between the maps are very small relative to the non-linearity in the element maps. Most outstanding is a maximally symmetric three cluster attractor in period three motion (MSCA) due to the foliation of the period three window of the element logistic maps. An analytic approach is proposed which explains successfully the systematics of various periodicity manifestations in the turbulent regime. The linear stability of the period three cluster attractors is investigated.Comment: 34 pages, 8 Postscript figures, all in GCML-MSCA.Zi

Synchronization and directed percolation in coupled map lattices

We study a synchronization mechanism, based on one-way coupling of all-or-nothing type, applied to coupled map lattices with several different local rules. By analyzing the metric and the topological distance between the two systems, we found two different regimes: a strong chaos phase in which the transition has a directed percolation character and a weak chaos phase in which the synchronization transition occurs abruptly. We are able to derive some analytical approximations for the location of the transition point and the critical properties of the system. We propose to use the characteristics of this transition as indicators of the spatial propagation of chaoticity.Comment: 12 pages + 12 figure