@article{3262,
  abstract     = {Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point.},
  author       = {Tkacik, Gasper and Walczak, Aleksandra and Bialek, William},
  journal      = { Physical Review E statistical nonlinear and soft matter physics },
  number       = {4},
  publisher    = {American Institute of Physics},
  title        = {{Optimizing information flow in small genetic networks. III. A self-interacting gene}},
  doi          = {10.1103/PhysRevE.85.041903},
  volume       = {85},
  year         = {2012},
}

@article{3274,
  abstract     = {A boundary element model of a tunnel running through horizontally layered soil with anisotropic material properties is presented. Since there is no analytical fundamental solution for wave propagation inside a layered orthotropic medium in 3D, the fundamental displacements and stresses have to be calculated numerically. In our model this is done in the Fourier domain with respect to space and time. The assumption of a straight tunnel with infinite extension in the x direction makes it possible to decouple the system for every wave number kx, leading to a 2.5D-problem, which is suited for parallel computation. The special form of the fundamental solution, resulting from our Fourier ansatz, and the fact, that the calculation of the boundary integral equation is performed in the Fourier domain, enhances the stability and efficiency of the numerical calculations.},
  author       = {Rieckh, Georg and Kreuzer, Wolfgang and Waubke, Holger and Balazs, Peter},
  journal      = { Engineering Analysis with Boundary Elements},
  number       = {6},
  pages        = {960 -- 967},
  publisher    = {Elsevier},
  title        = {{A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil}},
  doi          = {10.1016/j.enganabound.2011.12.014},
  volume       = {36},
  year         = {2012},
}

@article{3374,
  abstract     = {Genetic regulatory networks enable cells to respond to changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits has deepened our understanding of what kinds of computations genetic regulatory networks can perform, and with what reliability. These advances have motivated researchers to look for connections between the architecture and function of genetic regulatory networks. Transmitting information between a network's inputs and outputs has been proposed as one such possible measure of function, relevant in certain biological contexts. Here we summarize recent developments in the application of information theory to gene regulatory networks. We first review basic concepts in information theory necessary for understanding recent work. We then discuss the functional complexity of gene regulation, which arises from the molecular nature of the regulatory interactions. We end by reviewing some experiments that support the view that genetic networks responsible for early development of multicellular organisms might be maximizing transmitted 'positional information'.},
  author       = {Tkacik, Gasper and Walczak, Aleksandra},
  journal      = {Journal of Physics: Condensed Matter},
  number       = {15},
  publisher    = {IOP Publishing},
  title        = {{Information transmission in genetic regulatory networks a review}},
  doi          = {10.1088/0953-8984/23/15/153102},
  volume       = {23},
  year         = {2011},
}

@article{3384,
  abstract     = {Here we introduce a database of calibrated natural images publicly available through an easy-to-use web interface. Using a Nikon D70 digital SLR camera, we acquired about  six-megapixel images of Okavango Delta of Botswana, a tropical savanna habitat similar to where the human eye is thought to have evolved. Some sequences of images were captured unsystematically while following a baboon troop, while others were designed to vary a single parameter such as aperture, object distance, time of day or position on the horizon. Images are available in the raw RGB format and in grayscale. Images are also available in units relevant to the physiology of human cone photoreceptors, where pixel values represent the expected number of photoisomerizations per second for cones sensitive to long (L), medium (M) and short (S) wavelengths. This database is distributed under a Creative Commons Attribution-Noncommercial Unported license to facilitate research in computer vision, psychophysics of perception, and visual neuroscience.},
  author       = {Tkacik, Gasper and Garrigan, Patrick and Ratliff, Charles and Milcinski, Grega and Klein, Jennifer and Seyfarth, Lucia and Sterling, Peter and Brainard, David and Balasubramanian, Vijay},
  journal      = {PLoS One},
  number       = {6},
  publisher    = {Public Library of Science},
  title        = {{Natural images from the birthplace of the human eye}},
  doi          = {10.1371/journal.pone.0020409},
  volume       = {6},
  year         = {2011},
}