EEG alpha and theta time-frequency structure during a written mathematical task.

Since the first electroencephalogram (EEG) was obtained, there have been many possibilities to use it as a tool to access brain cognitive dynamics. Mathematical (Math) problem solving is one of the most important cortical processes, but it is still far from being well understood. EEG is an inexpensive and simple indirect measure of brain operation, but only recently has low-cost equipment (mobile EEG) allowed sophisticated analyses in non-clinical settings. The main purpose of this work is to study EEG activation during a Math task in a realistic environment, using mobile EEG. A matching pursuit (MP)-based signal analysis technique was employed, since MP properties render it a priori suitable to study induced EEG activity over long time sequences, when it is not tightly locked to a given stimulus. The study sample comprised sixty healthy volunteers. Unlike the majority of previous studies, subjects were studied in a sitting position with their eyes open. They completed a written Math task outside the EEG lab, wearing a mobile EEG device (EPOC+). Theta [4 Hz-7.5 Hz], alpha (7.5 Hz-13 Hz] and 0.5 Hz micro-bands in the [0.5 Hz-20 Hz] range were studied with a low-density stochastic MP dictionary. Over 1-min windows, ongoing EEG alpha and theta activity was decomposed into numerous MP atoms with median duration around 3 s, similar to the duration of induced, time-locked activity obtained with event-related (des)synchronization (ERS/ERD) studies. Relative to Rest, there was lower right-side and posterior MP alpha atom/min during Math, whereas MP theta atom/min was significantly higher on anteriorly located electrodes, especially on the left side. MP alpha findings were particularly significant on a narrow range around 10 Hz-10.5 Hz, consistent with FFT alpha peak findings from ERS/ERD studies. With a streamlined protocol, these results replicate previous findings of EEG alpha and theta activation obtained during Math tasks with different signal analysis techniques and in different time frames. The efficient application to real-world, noisy EEG data with a low-resolution stochastic MP dictionary shows that this technique is very encouraging. These results provide support for studies of mathematical cognition with mobile EEG and matching pursuit.

GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks.

SUMMARY: Network-level visualization of functional data is a key aspect of both analysis and understanding of biological systems. In a continuing effort to create clear and integrated visualizations that facilitate the gathering of novel biological insights despite the overwhelming complexity of data, we present here the GrAph LANdscape VisualizaTion (GALANT), a Cytoscape plugin that builds functional landscapes onto biological networks. By using GALANT, it is possible to project any type of numerical data onto a network to create a smoothed data map resembling the network layout. As a Cytoscape plugin, GALANT is further improved by the functionalities of Cytoscape, the popular bioinformatics package for biological network visualization and data integration. AVAILABILITY: http://www.lbbc.ibb.unesp.br/galant.

Triplet entropy analysis of hemagglutinin and neuraminidase sequences measures influenza virus phylodynamics.

The influenza virus has been a challenge to science due to its ability to withstand new environmental conditions. Taking into account the development of virus sequence databases, computational approaches can be helpful to understand virus behavior over time. Furthermore, they can suggest new directions to deal with influenza. This work presents triplet entropy analysis as a potential phylodynamic tool to quantify nucleotide organization of viral sequences. The application of this measure to segments of hemagglutinin (HA) and neuraminidase (NA) of H1N1 and H3N2 virus subtypes has shown some variability effects along timeline, inferring about virus evolution. Sequences were divided by year and compared for virus subtype (H1N1 and H3N2). The nonparametric Mann-Whitney test was used for comparison between groups. Results show that differentiation in entropy precedes differentiation in GC content for both groups. Considering the HA fragment, both triplet entropy as well as GC concentration show intersection in 2009, year of the recent pandemic. Some conclusions about possible flu evolutionary lines were drawn.

Bioinformatical and in vitro approaches to essential oil-induced matrix metalloproteinase inhibition.

CONTEXT: Essential oils carry diverse antimicrobial and anti-enzymatic properties. OBJECTIVE: Matrix metalloproteinase (MMP) inhibition characteristics of Salvia fruticosa Miller (Labiatae), Myrtus communis Linnaeus (Myrtaceae), Juniperus communis Linnaeus (Cupressaceae), and Lavandula stoechas Linnaeus (Labiatae) essential oils were evaluated. MATERIALS AND METHODS: Chemical compositions of the essential oils were analyzed by gas chromatography-mass spectrometry (GC-MS). Bioinformatical database analysis was performed by STRING 9.0 and STITCH 2.0 databases, and ViaComplex software. Antibacterial activity of essential oils against periodontopathogens was tested by the disc diffusion assay and the agar dilution method. Cellular proliferation and cytotoxicity were determined by commercial kits. MMP-2 and MMP-9 activities were measured by zymography. RESULTS: Bioinformatical database analyses, under a score of 0.4 (medium) and a prior correction of 0.0, gave rise to a model of protein (MMPs and tissue inhibitors of metalloproteinases) vs. chemical (essential oil components) interaction network; where MMPs and essential oil components interconnected through interaction with hydroxyl radicals, molecular oxygen, and hydrogen peroxide. Components from L. stoechas potentially displayed a higher grade of interaction with MMP-2 and -9. Although antibacterial and growth inhibitory effects of essential oils on the tested periodontopathogens were limited, all of them inhibited MMP-2 in vitro at concentrations of 1 and 5 µL/mL. Moreover, same concentrations of M. communis and L. stoechas also inhibited MMP-9. MMP-inhibiting concentrations of essential oils were not cytotoxic against keratinocytes. DISCUSSION AND CONCLUSION: We propose essential oils of being useful therapeutic agents as MMP inhibitors through a mechanism possibly based on their antioxidant potential.

Evolutionary plasticity determination by orthologous groups distribution.

BACKGROUND: Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the evolution are concerned to nucleotide sequence alterations in closely related species. However, the analysis of large scale data about the distribution of gene families in non-exclusively closely related species can provide insights on how plastic or how conserved a given gene family is. Here, we analyze the abundance and diversity of all Eukaryotic Clusters of Orthologous Groups (KOG) present in STRING database, resulting in a total of 4,850 KOGs. This dataset comprises 481,421 proteins distributed among 55 eukaryotes. RESULTS: We propose an index to evaluate the evolutionary plasticity and conservation of an orthologous group based on its abundance and diversity across eukaryotes. To further KOG plasticity analysis, we estimate the evolutionary distance average among all proteins which take part in the same orthologous group. As a result, we found a strong correlation between the evolutionary distance average and the proposed evolutionary plasticity index. Additionally, we found low evolutionary plasticity in Saccharomyces cerevisiae genes associated with inviability and Mus musculus genes associated with early lethality. At last, we plot the evolutionary plasticity value in different gene networks from yeast and humans. As a result, it was possible to discriminate among higher and lower plastic areas of the gene networks analyzed. CONCLUSIONS: The distribution of gene families brings valuable information on evolutionary plasticity which might be related with genetic plasticity. Accordingly, it is possible to discriminate among conserved and plastic orthologous groups by evaluating their abundance and diversity across eukaryotes.