On the nonlinear statistics of range image patches

In [A. B. Lee, K. S. Pedersen, and D. Mumford, Int. J. Comput. Vis., 54 (2003), pp. 83–103], the authors study the distributions of 3 × 3 patches from optical images and from range images. In [G. Carlsson, T. Ishkanov, V. de Silva, and A. Zomorodian, Int. J. Comput. Vis., 76 (2008), pp. 1–12], the authors apply computational topological tools to the data set of optical patches studied by Lee, Pedersen, and Mumford and find geometric structures for high density subsets. One high density subset is called the primary circle and essentially consists of patches with a line separating a light and a dark region. In this paper, we apply the techniques of Carlsson et al. to range patches. By enlarging to 5×5 and 7×7 patches, we find core subsets that have the topology of the primary circle, suggesting a stronger connection between optical patches and range patches than was found by Lee, Pedersen, and Mumford

The Nonlinear Statistics of High-Contrast Patches in Natural Images

Recently, there has been a great deal of interest in modeling the non-Gaussian structures of natural images. However, despite the many advances in the direction of sparse coding and multi-resolution analysis, the full probability distribution of pixels values in a neighborhood has not yet been described. In this study, we explore the space of data points representing the values of 3 × 3 high-contrast patches from optical and 3D range images. We find that the distribution of data is extremely “sparse” with the majority of the data points concentrated in clusters and non-linear low-dimensional manifolds. Furthermore, a detailed study of probability densities allows us to systematically distinguish between images of different modalities (optical versus range), which otherwise display similar marginal distributions. Our work indicates the importance of studying the full probability distribution of natural images, not just marginals, and the need to understand the intrinsic dimensionality and nature of the data. We believe that object-like structures in the world and the sensor properties of the probing device generate observations that are concentrated along predictable shapes in state space. Our study of natural image statistics accounts for local geometries (such as edges) in natural scenes, but does not impose such strong assumptions on the data as independent components or sparse coding by linear change of bases.Mathematic

Thermodynamics of Heat Shock Response

Production of heat shock proteins are induced when a living cell is exposed to a rise in temperature. The heat shock response of protein DnaK synthesis in E.coli for temperature shifts from temperature T to T plus 7 degrees, respectively to T minus 7 degrees is measured as function of the initial temperature T. We observe a reversed heat shock at low T. The magnitude of the shock increases when one increase the distance to the temperature $T_0 \approx 23^o$, thereby mimicking the non monotous stability of proteins at low temperature. Further we found that the variation of the heat shock with T quantitatively follows the thermodynamic stability of proteins with temperature. This suggest that stability related to hot as well as cold unfolding of proteins is directly implemented in the biological control of protein folding. We demonstrate that such an implementation is possible in a minimalistic chemical network.Comment: To be published in Physical Review Letter

Fish intake, erythrocyte n-3 fatty acid status and metabolic health in Danish adolescent girls and boys

Marinen-3 long-chain PUFA (n-3 LCPUFA) may have a beneficial effect on several aspects of the metabolic syndrome (dyslipidaemia, insulin resistance, hypertension and abdominal obesity). The metabolic syndrome is increasing in prevalence during adolescence, but only few studies have investigated the effects ofn-3 LCPUFA in adolescence. The present study examines associations between fish intake (assessed by a 7 d pre-coded food diary), erythrocyte (RBC) DHA status (analysed by GC) and metabolic syndrome measures (anthropometry, blood pressure and plasma lipids, insulin and glucose) in 109 17-year-old children from the Copenhagen Birth Cohort Study. Of the children, 8 % were overweight or obese and few showed signs of the metabolic syndrome, but all the metabolic syndrome variables were correlated. Median fish intake was 10·7 (interquartile range 3·6–21·2) g/d. Boys tended to have a higher fish intake (P = 0·052), but girls had significantly higher RBC levels of DHA (P = 0·001). Sex and fish intake explained 37 % of the variance in RBC-DHA (P &lt; 0·001). After adjusting for confounders, high DHA status was found to be significantly correlated with higher systolic blood pressure (P = 0·014) and increased fasting insulin (P = 0·018), but no adverse association was observed with the mean metabolic syndromez-score. Overall, the present study showed the expected association between fish intake and RBC-DHA, which in contrast to our expectations tended to be associated with a poorer metabolic profile. Whether these results reflect the physiological function ofn-3 LCPUFA, lifestyle factors associated with fish intake in Denmark, or mere chance remains to be investigated.</jats:p

UCE: A uracil excision (USER™)-based toolbox for transformation of cereals

<p>Abstract</p> <p>Background</p> <p>Cloning of gene casettes and other DNA sequences into the conventional vectors for biolistic or <it>Agrobacterium</it>-mediated transformation is hampered by a limited amount of unique restriction sites and by the difficulties often encountered when ligating small single strand DNA overhangs. These problems are obviated by "The Uracil Specific Excision Reagent (USER™)" technology (New England Biolabs) which thus offers a new and very time-efficient method for engineering of big and complex plasmids.</p> <p>Results</p> <p>By application of the USER™ system, we engineered a collection of binary vectors, termed UCE (USER cereal), ready for use in cloning of complex constructs into the T-DNA. A series of the vectors were tested and shown to perform successfully in <it>Agrobacterium</it>-mediated transformation of barley (<it>Hordeum vulgare </it>L.) as well as in biolistic transformation of endosperm cells conferring transient expression.</p> <p>Conclusions</p> <p>The USER™ technology is very well suited for generating a toolbox of vectors for transformation and it opens an opportunity to engineer complex vectors, where several genetic elements of different origin are combined in a single cloning reaction.</p

Fluorescence-based tracing of transplanted intestinal epithelial cells using confocal laser endomicroscopy

BACKGROUND: Intestinal stem cell transplantation has been shown to promote mucosal healing and to engender fully functional epithelium in experimental colitis. Hence, stem cell therapies may provide an innovative approach to accomplish mucosal healing in patients with debilitating conditions such as inflammatory bowel disease. However, an approach to label and trace transplanted cells, in order to assess engraftment efficiency and to monitor wound healing, is a key hurdle to overcome prior to initiating human studies. Genetic engineering is commonly employed in animal studies, but may be problematic in humans due to potential off-target and long-term adverse effects. METHODS: We investigated the applicability of a panel of fluorescent dyes and nanoparticles to label intestinal organoids for visualization using the clinically approved imaging modality, confocal laser endomicroscopy (CLE). Staining homogeneity, durability, cell viability, differentiation capacity, and organoid forming efficiency were evaluated, together with visualization of labeled organoids in vitro and ex vivo using CLE. RESULTS: 5-Chloromethylfluorescein diacetate (CMFDA) proved to be suitable as it efficiently stained all organoids without transfer to unstained organoids in co-cultures. No noticeable adverse effects on viability, organoid growth, or stem cell differentiation capacity were observed, although single-cell reseeding revealed a dose-dependent reduction in organoid forming efficiency. Labeled organoids were easily identified in vitro using CLE for a duration of at least 3 days and could additionally be detected ex vivo following transplantation into murine experimental colitis. CONCLUSIONS: It is highly feasible to use fluorescent dye-based labeling in combination with CLE to trace intestinal organoids following transplantation to confirm implantation at the intestinal target site

Theory of Flux-Flow Resistivity near Hc2H_{c2} for s-wave Type-II Superconductors

This paper presents a microscopic calculation of the flux-flow resistivity $\rho_{f}$ for s-wave type-II superconductors with arbitrary impurity concentrations near the upper critical field $H_{c2}$. It is found that, as the mean free path $l$ becomes longer, $\rho_{f}$ increases gradually from the dirty-limit result of Thompson [Phys. Rev. B{\bf 1}, 327 (1970)] and Takayama and Ebisawa [Prog. Theor. Phys. {\bf 44}, 1450 (1970)]. The limiting behaviors suggest that $\rho_{f}(H)$ at low temperatures may change from convex downward to upward as $l$ increases, thus deviating substantially from the linear dependence $\rho_{f}\propto H/H_{c2}$ predicted by the Bardeen-Stephen theory [Phys. Rev. {\bf 140}, A1197 (1965)]

Controllability and universal three-qubit quantum computation with trapped electron states

We show how to control and perform universal three-qubit quantum computation with trapped electron quantum states. The three qubits are the electron spin, and the first two quantum states of the cyclotron and axial harmonic oscillators. We explicitly show how the universal gates can be performed. As an example of a non-trivial quantum algorithm, we outline the implementation of the Deutsch-Jozsa algorithm in this system.Comment: 4 pages, 1 figure. Typos corrected. The original publication is available at http://www.springerlink.co

Cosmological Systematics Beyond Nuisance Parameters : Form Filling Functions

In the absence of any compelling physical model, cosmological systematics are often misrepresented as statistical effects and the approach of marginalising over extra nuisance systematic parameters is used to gauge the effect of the systematic. In this article we argue that such an approach is risky at best since the key choice of function can have a large effect on the resultant cosmological errors. As an alternative we present a functional form filling technique in which an unknown, residual, systematic is treated as such. Since the underlying function is unknown we evaluate the effect of every functional form allowed by the information available (either a hard boundary or some data). Using a simple toy model we introduce the formalism of functional form filling. We show that parameter errors can be dramatically affected by the choice of function in the case of marginalising over a systematic, but that in contrast the functional form filling approach is independent of the choice of basis set. We then apply the technique to cosmic shear shape measurement systematics and show that a shear calibration bias of |m(z)|< 0.001(1+z)^0.7 is required for a future all-sky photometric survey to yield unbiased cosmological parameter constraints to percent accuracy. A module associated with the work in this paper is available through the open source iCosmo code available at http://www.icosmo.org .Comment: 24 pages, 18 figures, accepted to MNRA