Coherent Signal Amplification in Bistable Nanomechanical Oscillators by Stochastic Resonance

Stochastic resonance is a counter-intuitive concept[1,2], ; the addition of noise to a noisy system induces coherent amplification of its response. First suggested as a mechanism for the cyclic recurrence of ice ages, stochastic resonance has been seen in a wide variety of macroscopic physical systems: bistable ring lasers[3], SQUIDs[4,5], magnetoelastic ribbons[6], and neurophysiological systems such as the receptors in crickets[7] and crayfish[8]. Although it is fundamentally important as a mechanism of coherent signal amplification, stochastic resonance is yet to be observed in nanoscale systems. Here we report the observation of stochastic resonance in bistable nanomechanical silicon oscillators, which can play an important role in the realization of controllable high-speed nanomechanical memory cells. Our nanomechanical systems were excited into a dynamic bistable state and modulated in order to induce controllable switching; the addition of white noise showed a marked amplification of the signal strength. Stochastic resonance in nanomechanical systems paves the way for exploring macroscopic quantum coherence and tunneling, and controlling nanoscale quantum systems for their eventual use as robust quantum logic devices.Comment: 18 pages, 4 figure

Local population and regional environmental drivers of cholera in Bangladesh

<p>Abstract</p> <p>Background</p> <p>Regional environmental factors have been shown to be related to cholera. Previous work in Bangladesh found that temporal patterns of cholera are positively related to satellite-derived environmental variables including ocean chlorophyll concentration (OCC).</p> <p>Methods</p> <p>This paper investigates whether local socio-economic status (SES) modifies the effect of regional environmental forces. The study area is Matlab, Bangladesh, an area of approximately 200,000 people with an active health and demographic surveillance system. Study data include (1) spatially-referenced demographic and socio-economic characteristics of the population; (2) satellite-derived variables for sea surface temperature (SST), sea surface height (SSH), and OCC; and (3) laboratory confirmed cholera case data for the entire population. Relationships between cholera, the environmental variables, and SES are measured using generalized estimating equations with a logit link function. Additionally two separate seasonal models are built because there are two annual cholera epidemics, one pre-monsoon, and one post-monsoon.</p> <p>Results</p> <p>SES has a significant impact on cholera occurrence: the higher the SES score, the lower the occurrence of cholera. There is a significant negative association between cholera incidence and SSH during the pre-monsoon period but not for the post-monsoon period. OCC is positively associated with cholera during the pre-monsoon period but not for the post-monsoon period. SST is not related to cholera incidence.</p> <p>Conclusions</p> <p>Overall, it appears cholera is influenced by regional environmental variables during the pre-monsoon period and by local-level variables (e.g., water and sanitation) during the post-monsoon period. In both pre- and post-monsoon seasons, SES significantly influences these patterns, likely because it is a proxy for poor water quality and sanitation in poorer households.</p

bioNMF: a versatile tool for non-negative matrix factorization in biology

BACKGROUND: In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the complex latent relationships in experimental data sets. This method, and some of its variants, has been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even if the interest on this technique by the bioinformatics community has been increased during the last few years, there are not many available simple standalone tools to specifically perform these types of data analysis in an integrated environment. RESULTS: In this work we propose a versatile and user-friendly tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications of this new methodology. This includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification using gene expression. The tool, which is named bioNMF, also contains a user-friendly graphical interface to explore results in an interactive manner and facilitate in this way the exploratory data analysis process. CONCLUSION: bioNMF is a standalone versatile application which does not require any special installation or libraries. It can be used for most of the multiple applications proposed in the bioinformatics field or to support new research using this method. This tool is publicly available at

Optimality of mutation and selection in germinal centers

The population dynamics theory of B cells in a typical germinal center could play an important role in revealing how affinity maturation is achieved. However, the existing models encountered some conflicts with experiments. To resolve these conflicts, we present a coarse-grained model to calculate the B cell population development in affinity maturation, which allows a comprehensive analysis of its parameter space to look for optimal values of mutation rate, selection strength, and initial antibody-antigen binding level that maximize the affinity improvement. With these optimized parameters, the model is compatible with the experimental observations such as the ~100-fold affinity improvements, the number of mutations, the hypermutation rate, and the "all or none" phenomenon. Moreover, we study the reasons behind the optimal parameters. The optimal mutation rate, in agreement with the hypermutation rate in vivo, results from a tradeoff between accumulating enough beneficial mutations and avoiding too many deleterious or lethal mutations. The optimal selection strength evolves as a balance between the need for affinity improvement and the requirement to pass the population bottleneck. These findings point to the conclusion that germinal centers have been optimized by evolution to generate strong affinity antibodies effectively and rapidly. In addition, we study the enhancement of affinity improvement due to B cell migration between germinal centers. These results could enhance our understandings to the functions of germinal centers.Comment: 5 figures in main text, and 4 figures in Supplementary Informatio

Complex temporal climate signals drive the emergence of human water-borne disease

Predominantly occurring in developing parts of the world, Buruli ulcer is a severely disabling mycobacterium infection which often leads to extensive necrosis of the skin. While the exact route of transmission remains uncertain, like many tropical diseases, associations with climate have been previously observed and could help identify the causative agent's ecological niche. In this paper, links between changes in rainfall and outbreaks of Buruli ulcer in French Guiana, an ultraperipheral European territory in the northeast of South America, were identified using a combination of statistical tests based on singular spectrum analysis, empirical mode decomposition and cross-wavelet coherence analysis. From this, it was possible to postulate for the first time that outbreaks of Buruli ulcer can be triggered by combinations of rainfall patterns occurring on a long (i.e., several years) and short (i.e., seasonal) temporal scale, in addition to stochastic events driven by the El Nino-Southern Oscillation that may disrupt or interact with these patterns. Long-term forecasting of rainfall trends further suggests the possibility of an upcoming outbreak of Buruli ulcer in French Guiana

From Antenna to Antenna: Lateral Shift of Olfactory Memory Recall by Honeybees

Honeybees, Apis mellifera, readily learn to associate odours with sugar rewards and we show here that recall of the olfactory memory, as demonstrated by the bee extending its proboscis when presented with the trained odour, involves first the right and then the left antenna. At 1–2 hour after training using both antennae, recall is possible mainly when the bee uses its right antenna but by 6 hours after training a lateral shift has occurred and the memory can now be recalled mainly when the left antenna is in use. Long-term memory one day after training is also accessed mainly via the left antenna. This time-dependent shift from right to left antenna is also seen as side biases in responding to odour presented to the bee's left or right side. Hence, not only are the cellular events of memory formation similar in bees and vertebrate species but also the lateralized networks involved may be similar. These findings therefore seem to call for remarkable parallel evolution and suggest that the proper functioning of memory formation in a bilateral animal, either vertebrate or invertebrate, requires lateralization of processing

Chemical composition and antigenotoxic properties of Lippia alba essential oils

The present work evaluated the chemical composition and the DNA protective effect of the essential oils (EOs) from Lippia alba against bleomycin-induced genotoxicity. EO constituents were determined by Gas Chromatography/Mass Spectrometric (GC-MS) analysis. The major compounds encountered being citral (33% geranial and 25% neral), geraniol (7%) and trans-β-caryophyllene (7%) for L. alba specimen COL512077, and carvone (38%), limonene (33%) and bicyclosesquiphellandrene (8%) for the other, COL512078. The genotoxicity and antigenotoxicity of EO and the compounds citral, carvone and limonene, were assayed using the SOS Chromotest in Escherichia coli. The EOs were not genotoxic in the SOS chromotest, but one of the major compound (limonene) showed genotoxicity at doses between 97 and 1549 mM. Both EOs protected bacterial cells against bleomycin-induced genotoxicity. Antigenotoxicity in the two L. alba chemotypes was related to the major compounds, citral and carvone, respectively. The results were discussed in relation to the chemopreventive potential of L. alba EOs and its major compounds

Neural Substrates for the Motivational Regulation of Motor Recovery after Spinal-Cord Injury

It is believed that depression impedes and motivation enhances functional recovery after neuronal damage such as spinal-cord injury and stroke. However, the neuronal substrate underlying such psychological effects on functional recovery remains unclear. A longitudinal study of brain activation in the non-human primate model of partial spinal-cord injury using positron emission tomography (PET) revealed a contribution of the primary motor cortex (M1) to the recovery of finger dexterity through the rehabilitative training. Here, we show that activity of the ventral striatum, including the nucleus accumbens (NAc), which plays a critical role in processing of motivation, increased and its functional connectivity with M1 emerged and was progressively strengthened during the recovery. In addition, functional connectivities among M1, the ventral striatum and other structures belonging to neural circuits for processing motivation, such as the orbitofrontal cortex, anterior cingulate cortex and pedunculopontine tegmental nucleus were also strengthened during the recovery. These results give clues to the neuronal substrate for motivational regulation of motor learning required for functional recovery after spinal-cord injury