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Information Storage and Retrieval for Probe Storage using Optical Diffraction Patterns  [PDF]
Joost van Honschoten,Henri de Jong,Wabe W. Koelmans,Thomas P. Parnell,Oleg V. Zaboronski
Mathematics , 2011, DOI: 10.1063/1.3657945
Abstract: A novel method for fast information retrieval from a probe storage device is considered. It is shown that information can be stored and retrieved using the optical diffraction patterns obtained by the illumination of a large array of cantilevers by a monochromatic light source. In thermo-mechanical probe storage, the information is stored as a sequence of indentations on the polymer medium. To retrieve the information, the array of probes is actuated by applying a bending force to the cantilevers. Probes positioned over indentations experience deflection by the depth of the indentation, probes over the flat media remain un-deflected. Thus the array of actuated probes can be viewed as an irregular optical grating, which creates a data-dependent diffraction pattern when illuminated by laser light. We develop a low complexity modulation scheme, which allows the extraction of information stored in the pattern of indentations on the media from Fourier coefficients of the intensity of the diffraction pattern. We then derive a low-complexity maximum likelihood sequence detection algorithm for retrieving the user information from the Fourier coefficients. The derivation of both the modulation and the detection schemes is based on the Fraunhofer formula for data-dependent diffraction patterns. We show that for as long as the Fresnel number F<0.1, the optimal channel detector derived from Fraunhofer diffraction theory does not suffer any significant performance degradation.
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mari?o-Ramírez, John L Spouge
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-262
Abstract: A-GLAM, a user-friendly computer program for identifying sequence motifs, now incorporates a Bayesian model systematically combining sequence and positional information. A-GLAM's predictions with and without positional information were compared on two human TFBS datasets, each containing sequences corresponding to the interval [-2000, 0] bases upstream of a known TSS. A rigorous statistical analysis showed that positional information significantly improved the prediction of sequence motifs, and an extensive cross-validation study showed that A-GLAM's model was robust against mild misspecification of its parameters. As expected, when sequences in the datasets were successively truncated to the intervals [-1000, 0], [-500, 0] and [-250, 0], positional information aided motif prediction less and less, but never hurt it significantly.Although sequence truncation is a viable strategy when searching for biologically active motifs with a positional preference, a probabilistic model (used reasonably) generally provides a superior and more robust strategy, particularly when the sequence motifs' positional preferences are not well characterized.Transcription factor binding sites (TFBSs) provide a specific example of biologically functional sequence motifs that sometimes have positional preferences. TFBSs contribute substantially to the control of gene expression, and because of their biological importance, much experimental effort has been expended in identifying them. Because experimental identification is expensive, there are now many computational tools that identify TFBSs as the subsequences, or "motifs", common to a set of sequences. Most TFBSs correspond to short and imprecise motifs [1], however, so all computational tools in a recent contest performed rather poorly in identifying known TFBSs [2].Although some tools have an ad hoc basis [3-5], other tools have a basis in the calculus of probability, and can therefore immediately and systematically combine sequence with
Positional information, in bits  [PDF]
Julien O. Dubuis,Gasper Tkacik,Eric F. Wieschaus,Thomas Gregor,William Bialek
Quantitative Biology , 2011,
Abstract: Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.
Positional information, positional error, and read-out precision in morphogenesis: a mathematical framework  [PDF]
Ga?per Tka?ik,Julien O Dubuis,Mariela D Petkova,Thomas Gregor
Physics , 2014,
Abstract: The concept of positional information is central to our understanding of how cells in a multicellular structure determine their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine which features of expression patterns increase or decrease positional information. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with single cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail.
Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively  [PDF]
Jacob Clifford,Christoph Adami
Quantitative Biology , 2015, DOI: 10.1088/1478-3975/12/5/056004
Abstract: Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through Position Weight Matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each site's locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal-Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.
Positional accuracy of geographical information and recent standards for its evaluation  [PDF]
Radoj?i? Stevan,Borisov Mirko,Bo?i? Branko
Glasnik Srpskog Geografskog Dru?tva , 2011, DOI: 10.2298/gsgd1102099r
Abstract: Positional accuracy is important quantity element of quality of geographical information in digital as well as in analoguos form. This paper points to importance and necessity of evaluation of positional accuracy in recent conditions, describes two modern standards for positional accuracy evaluation and shows the results of its implementation on raster topographic map at scale 1:50.000 made by Military Geographical Institute.
Emerging Patterns and Classification Algorithms for DNA Sequence  [cached]
Xiaoyun Chen,Jinhua Chen
Journal of Software , 2011, DOI: 10.4304/jsw.6.6.985-992
Abstract: Existing machine learning methods for classification of DNA sequence achieve good results, but these methods try to express a DNA sequences as discrete multi-dimensional vector, so when the length of the sequences in the DNA sequence database is not fixed or there exists some omitted characters, these methods can not be used directly. In this paper, we define the new support and growth rate of support to find the frequent emerging patterns from DNA sequence database, and present a classification algorithm FESP based on the frequent emerging sequence patterns. The frequent emerging sequence patterns keep the information provided by the order of bases in gene sequences and can catch interaction among bases. FESP algorithm applies classification rules that are constructed by frequent emerging sequence patterns of each class to classify the new DNA sequences. This method can work on sequences with different lengths or omitted character and shows good performance.
Two-Player Perfect-Information Shift-Invariant Submixing Stochastic Games Are Half-Positional  [PDF]
Hugo Gimbert,Edon Kelmendi
Computer Science , 2014,
Abstract: We consider zero-sum stochastic games with perfect information and finitely many states and actions. The payoff is computed by a payoff function which associates to each infinite sequence of states and actions a real number. We prove that if the the payoff function is both shift-invariant and submixing, then the game is half-positional, i.e. the first player has an optimal strategy which is both deterministic and stationary. This result relies on the existence of $\epsilon$-subgame-perfect equilibria in shift-invariant games, a second contribution of the paper.
Storage of correlated patterns in a perceptron  [PDF]
B. Lopez,M. Schroeder,M. Opper
Physics , 1995, DOI: 10.1088/0305-4470/28/16/005
Abstract: We calculate the storage capacity of a perceptron for correlated gaussian patterns. We find that the storage capacity $\alpha_c$ can be less than 2 if similar patterns are mapped onto different outputs and vice versa. As long as the patterns are in general position we obtain, in contrast to previous works, that $\alpha_c \geq 1$ in agreement with Cover's theorem. Numerical simulations confirm the results.
Positional Information Is Reprogrammed in Blastema Cells of the Regenerating Limb of the Axolotl (Ambystoma mexicanum)  [PDF]
Catherine D. McCusker, David M. Gardiner
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0077064
Abstract: The regenerating region of an amputated salamander limb, known as the blastema, has the amazing capacity to replace exactly the missing structures. By grafting cells from different stages and regions of blastemas induced to form on donor animals expressing Green Fluorescent Protein (GFP), to non-GFP host animals, we have determined that the cells from early stage blastemas, as well as cells at the tip of late stage blastemas are developmentally labile such that their positional identity is reprogrammed by interactions with more proximal cells with stable positional information. In contrast, cells from the adjacent, more proximal stump tissues as well as the basal region of late bud blastemas are positionally stable, and thus form ectopic limb structures when grafted. Finally, we have found that a nerve is required to maintain the blastema cells in a positionally labile state, thus indicating a role for reprogramming cues in the blastema microenvironment.
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