Nonlinear propagation of an optical speckle field

We provide a theoretical explanation of the results on the intensity distributions and correlation functions obtained from a random-beam speckle field in nonlinear bulk waveguides reported in the recent publication by Bromberg et al. [Nat. Photonics 4, 721 (2010) ].. We study both the focusing and defocusing cases and in the limit of small speckle size (short-correlated disordered beam) provide analytical asymptotes for the intensity probability distributions at the output facet. Additionally we provide a simple relation between the speckle sizes at the input and output of a focusing nonlinear waveguide. The results are of practical significance for nonlinear Hanbury Brown and Twiss interferometry in both optical waveguides and Bose-Einstein condensates

Spectral control of broadband light through random media by wavefront shaping

A random medium can serve as a controllable arbitrary spectral filter with spectral resolution determined by the inverse of the interaction time of the light in the medium. We use wavefront shaping to implement an arbitrary spectral response at a particular point in the scattered field. We experimentally demonstrate this technique by selecting either a narrow band or dual bands with a width of 5.5nm each

Polarization control of multiply-scattered light through random media by wavefront shaping

We show that the polarization state of coherent light propagating through an optically thick multiple-scattering medium, can be controlled by wavefront shaping, i.e. by controlling only the spatial phase of the incoming field with a spatial light modulator. Any polarization state of light at any spatial position behind the scattering medium can be attained with this technique. Thus, transforming the random medium to an arbitrary optical polarization component becomes possible

Focusing and Compression of Ultrashort Pulses through Scattering Media

Light scattering in inhomogeneous media induces wavefront distortions which pose an inherent limitation in many optical applications. Examples range from microscopy and nanosurgery to astronomy. In recent years, ongoing efforts have made the correction of spatial distortions possible by wavefront shaping techniques. However, when ultrashort pulses are employed scattering induces temporal distortions which hinder their use in nonlinear processes such as in multiphoton microscopy and quantum control experiments. Here we show that correction of both spatial and temporal distortions can be attained by manipulating only the spatial degrees of freedom of the incident wavefront. Moreover, by optimizing a nonlinear signal the refocused pulse can be shorter than the input pulse. We demonstrate focusing of 100fs pulses through a 1mm thick brain tissue, and 1000-fold enhancement of a localized two-photon fluorescence signal. Our results open up new possibilities for optical manipulation and nonlinear imaging in scattering media

Presymptomatic risk assessment for chronic non-communicable diseases

The prevalence of common chronic non-communicable diseases (CNCDs) far overshadows the prevalence of both monogenic and infectious diseases combined. All CNCDs, also called complex genetic diseases, have a heritable genetic component that can be used for pre-symptomatic risk assessment. Common single nucleotide polymorphisms (SNPs) that tag risk haplotypes across the genome currently account for a non-trivial portion of the germ-line genetic risk and we will likely continue to identify the remaining missing heritability in the form of rare variants, copy number variants and epigenetic modifications. Here, we describe a novel measure for calculating the lifetime risk of a disease, called the genetic composite index (GCI), and demonstrate its predictive value as a clinical classifier. The GCI only considers summary statistics of the effects of genetic variation and hence does not require the results of large-scale studies simultaneously assessing multiple risk factors. Combining GCI scores with environmental risk information provides an additional tool for clinical decision-making. The GCI can be populated with heritable risk information of any type, and thus represents a framework for CNCD pre-symptomatic risk assessment that can be populated as additional risk information is identified through next-generation technologies.Comment: Plos ONE paper. Previous version was withdrawn to be updated by the journal's pdf versio

Studying the functional conservation of cis-regulatory modules and their transcriptional output

<p>Abstract</p> <p>Background</p> <p><it>Cis</it>-regulatory modules (CRMs) are distinct, genomic regions surrounding the target gene that can independently activate the promoter to drive transcription. The activation of a CRM is controlled by the binding of a certain combination of transcription factors (TFs). It would be of great benefit if the transcriptional output mediated by a specific CRM could be predicted. Of equal benefit would be identifying <it>in silico </it>a specific CRM as the driver of the expression in a specific tissue or situation. We extend a recently developed biochemical modeling approach to manage both prediction tasks. Given a set of TFs, their protein concentrations, and the positions and binding strengths of each of the TFs in a putative CRM, the model predicts the transcriptional output of the gene. Our approach predicts the location of the regulating CRM by using predicted TF binding sites in regions near the gene as input to the model and searching for the region that yields a predicted transcription rate most closely matching the known rate.</p> <p>Results</p> <p>Here we show the ability of the model on the example of one of the CRMs regulating the <it>eve </it>gene, MSE2. A model trained on the MSE2 in <it>D. melanogaster </it>was applied to the surrounding sequence of the <it>eve </it>gene in seven other <it>Drosophila </it>species. The model successfully predicts the correct MSE2 location and output in six out of eight <it>Drosophila </it>species we examine.</p> <p>Conclusion</p> <p>The model is able to generalize from <it>D. melanogaster </it>to other <it>Drosophila </it>species and accurately predicts the location and transcriptional output of MSE2 in those species. However, we also show that the current model is not specific enough to function as a genome-wide CRM scanner, because it incorrectly predicts other genomic regions to be MSE2s.</p