WAVOS: a MATLAB toolkit for wavelet analysis and visualization of oscillatory systems

<p>Abstract</p> <p>Background</p> <p>Wavelets have proven to be a powerful technique for the analysis of periodic data, such as those that arise in the analysis of circadian oscillators. While many implementations of both continuous and discrete wavelet transforms are available, we are aware of no software that has been designed with the nontechnical end-user in mind. By developing a toolkit that makes these analyses accessible to end users without significant programming experience, we hope to promote the more widespread use of wavelet analysis.</p> <p>Findings</p> <p>We have developed the WAVOS toolkit for wavelet analysis and visualization of oscillatory systems. WAVOS features both the continuous (Morlet) and discrete (Daubechies) wavelet transforms, with a simple, user-friendly graphical user interface within MATLAB. The interface allows for data to be imported from a number of standard file formats, visualized, processed and analyzed, and exported without use of the command line. Our work has been motivated by the challenges of circadian data, thus default settings appropriate to the analysis of such data have been pre-selected in order to minimize the need for fine-tuning. The toolkit is flexible enough to deal with a wide range of oscillatory signals, however, and may be used in more general contexts.</p> <p>Conclusions</p> <p>We have presented WAVOS: a comprehensive wavelet-based MATLAB toolkit that allows for easy visualization, exploration, and analysis of oscillatory data. WAVOS includes both the Morlet continuous wavelet transform and the Daubechies discrete wavelet transform. We have illustrated the use of WAVOS, and demonstrated its utility for the analysis of circadian data on both bioluminesence and wheel-running data. WAVOS is freely available at <url>http://sourceforge.net/projects/wavos/files/</url></p

Testing nowcasts of the ionospheric convection from the expanding and contracting polar cap model

The expanding/contracting polar cap (ECPC) model, or the time-dependent Dungey cycle, provides a theoretical framework for understanding solar wind-magnetosphere-ionosphere coupling. The ECPC describes the relationship between magnetopause reconnection and substorm growth phase, magnetotail reconnection and substorm expansion phase, associated changes in auroral morphology, and ionospheric convective motions. Despite the many successes of the model, there has yet to be a rigorous test of the predictions or nowcasts made regarding ionospheric convection, which remains a final hurdle for the validation of the ECPC. In this study we undertake a comparison of ionospheric convection, as measured in situ by ion drift meters on board DMSP (Defense Meteorological Satellite Program) satellites and from the ground by SuperDARN (Super Dual Auroral Radar Network), with motions nowcasted by a theoretical model. The model is coupled to measurements of changes in the size of the polar cap made using global auroral imagery from the IMAGE FUV (Imager for Magnetopause to Aurora Global Exploration Far Ultraviolet) instrument, as well as the dayside reconnection rate, estimated using the OMNI data set. The results show that we can largely nowcast the magnitudes of ionospheric convection flows using the context of our understanding of magnetic reconnection at the magnetopause and in the magnetotail

The emerging landscape of health research based on biobanks linked to electronic health records: Existing resources, statistical challenges, and potential opportunities

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154448/1/sim8445_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154448/2/sim8445.pd

Kelvin-Helmholtz instability in the presence of variable viscosity for mudflow resuspension in estuaries

The temporal stability of a parallel shear flow of miscible fluid layers of dif- ferent density and viscosity is investigated through a linear stability analysis and direct numerical simulations. The geometry and rheology of this Newto- nian fluid mixing can be viewed as a simplified model of the behavior of mud- flow at the bottom of estuaries for suspension studies. In this study, focus is on the stability and transition to turbulence of an initially laminar configuration. A parametric analysis is performed by varying the values of three control pa- rameters, namely the viscosity ratio, the Richardson and Reynolds numbers, in the case of initially identical thickness of the velocity, density and viscosity profiles. The range of parameters has been chosen so as to mimic a wide variety of real configurations. This study shows that the Kelvin-Helmholtz instability is controlled by the local Reynolds and Richardson numbers of the inflection point. In addition, at moderate Reynolds number, viscosity strat- ification has a strong influence on the onset of instability, the latter being enhanced at high viscosity ratio, while at high Reynolds number, the influ- ence is less pronounced. In all cases, we show that the thickness of the mixing layer (and thus resuspension) is increased by high viscosity stratification, in particular during the non-linear development of the instability and especially pairing processes. This study suggests that mud viscosity has to be taken into account for resuspension parameterizations because of its impact on the inflec- tion point Reynolds number and the viscosity ratio, which are key parameters for shear instabilities

De-anonymizing programmers via code stylometry

© 2015 Proceedings of the 24th USENIX Security Symposium. All rights reserved. Source code authorship attribution is a significant privacy threat to anonymous code contributors. However, it may also enable attribution of successful attacks from code left behind on an infected system, or aid in resolving copyright, copyleft, and plagiarism issues in the programming fields. In this work, we investigate machine learning methods to de-anonymize source code authors of C/C++ using coding style. Our Code Stylometry Feature Set is a novel representation of coding style found in source code that reflects coding style from properties derived from abstract syntax trees. Our random forest and abstract syntax tree-based approach attributes more authors (1,600 and 250) with significantly higher accuracy (94% and 98%) on a larger data set (Google Code Jam) than has been previously achieved. Furthermore, these novel features are robust, difficult to obfuscate, and can be used in other programming languages, such as Python. We also find that (i) the code resulting from difficult programming tasks is easier to attribute than easier tasks and (ii) skilled programmers (who can complete the more difficult tasks) are easier to attribute than less skilled programmers

Log File Analysis with Context-Free Grammars

Part 3: FORENSIC TECHNIQUESInternational audienceClassical intrusion analysis of network log files uses statistical machine learning or regular expressions. Where statistically machine learning methods are not analytically exact, methods based on regular expressions do not reach up very far in Chomsky’s hierarchy of languages. This paper focuses on parsing traces of network traffic using context-free grammars. “Green grammars” are used to describe acceptable log files while “red grammars” are used to represent known intrusion patterns. This technique can complement or augment existing approaches by providing additional precision. Analytically, the technique is also more powerful than existing techniques that use regular expressions

A neuropeptide speeds circadian entrainment by reducing intercellular synchrony.

Shift work or transmeridian travel can desynchronize the body's circadian rhythms from local light-dark cycles. The mammalian suprachiasmatic nucleus (SCN) generates and entrains daily rhythms in physiology and behavior. Paradoxically, we found that vasoactive intestinal polypeptide (VIP), a neuropeptide implicated in synchrony among SCN cells, can also desynchronize them. The degree and duration of desynchronization among SCN neurons depended on both the phase and the dose of VIP. A model of the SCN consisting of coupled stochastic cells predicted both the phase- and the dose-dependent response to VIP and that the transient phase desynchronization, or "phase tumbling", could arise from intrinsic, stochastic noise in small populations of key molecules (notably, Period mRNA near its daily minimum). The model also predicted that phase tumbling following brief VIP treatment would accelerate entrainment to shifted environmental cycles. We tested this using a prepulse of VIP during the day before a shift in either a light cycle in vivo or a temperature cycle in vitro. Although VIP during the day does not shift circadian rhythms, the VIP pretreatment approximately halved the time required for mice to reentrain to an 8-h shifted light schedule and for SCN cultures to reentrain to a 10-h shifted temperature cycle. We conclude that VIP below 100 nM synchronizes SCN cells and above 100 nM reduces synchrony in the SCN. We show that exploiting these mechanisms that transiently reduce cellular synchrony before a large shift in the schedule of daily environmental cues has the potential to reduce jet lag