Processing and Transmission of Information

Contains reports on one research project.Joint Services Electronics Programs (U. S. Army, U. S. Navy, and U. S. Air Force) under Contract DA 28-043-AMC-02536(E)Project MAC, an M.I.T. research program sponsored by the Advanced Research Projects Agency, Department of Defense, under Office of Naval Research Contract Nonr-4102(01

Response of mouse epidermal cells to single doses of heavy-particles

The survival of mouse epidermal cells to heavy-particles has been studied In Vivo by the Withers clone technique. Experiments with accelerated helium, lithium and carbon ions were performed. The survival curve for the helium ion irradiations used a modified Bragg curve method with a maximum tissue penetration of 465 microns, and indicated that the dose needed to reduce the original cell number to 1 surviving cell/square centimeters was 1525 rads with a D sub o of 95 rads. The LET at the basal cell layer was 28.6 keV per micron. Preliminary experiments with lithium and carbon used treatment doses of 1250 rads with LET's at the surface of the skin of 56 and 193 keV per micron respectively. Penetration depths in skin were 350 and 530 microns for the carbon and lithium ions whose Bragg curves were unmodified. Results indicate a maximum RBE for skin of about 2 using the skin cloning technique. An attempt has been made to relate the epidermal cell survival curve to mortality of the whole animal for helium ions

Contribution of cod liver oil-related nutrients (vitamins A, D, E and eicosapentaenoic acid and docosahexaenoic acid) to daily nutrient intake and their associations with plasma concentrations in the EPIC-Norfolk cohort

Total nutrient intake (TNI) is intake from food and supplements. This provides an assessment of nutrient adequacy and the prevalence of excessive intake, as well as the response with respect to biomarkers. Cod liver oil (CLO) is the most frequently consumed supplement in the UK, containing nutrients that might have varying influences on health. We calculated TNI for vitamins A, D and E, as well as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), and assessed associations with the respective blood concentrations

Single-Scattering Optical Tomography: Simultaneous Reconstruction of Scattering and Absorption

We demonstrate that simultaneous reconstruction of scattering and absorption of a mesoscopic system using angularly-resolved measurements of scattered light intensity is possible. Image reconstruction is realized based on the algebraic inversion of a generalized Radon transform relating the scattering and absorption coefficients of the medium to the measured light intensity and derived using the single-scattering approximation to the radiative transport equation.Comment: This is a sequel to physics/070311

Bayesian total evidence dating reveals the recent crown radiation of penguins

The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples. The fossilized birth-death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ~12.7 Ma and most splits leading to extant species occurring in the last 2 million years. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (v. 2.4) www.beast2.org with packages SA (v. at least 1.1.4) and morph-models (v. at least 1.0.4).Comment: 50 pages, 6 figure

Light scattering study of the “pseudo-layer” compression elastic constant in a twist-bend nematic liquid crystal

The nematic twist-bend (TB) phase, exhibited by certain achiral thermotropic liquid crystalline (LC) dimers, features a nanometer-scale, heliconical rotation of the average molecular long axis (director) with equally probable left- and right-handed domains. On meso to macroscopic scales, the TB phase may be considered as a stack of equivalent slabs or “pseudo-layers”, each one helical pitch in thickness. The long wavelength fluctuation modes should then be analogous to those of a smectic-A phase, and in particular the hydrodynamic mode combining “layer” compression and bending ought to be characterized by an effective layer compression elastic constant Beff and average director splay constant Keff1. The magnitude of Keff1 is expected to be similar to the splay constant of an ordinary nematic LC, but due to the absence of a true mass density wave, Beff could differ substantially from the typical value of ∼10⁶ Pa in a conventional smectic-A. Here we report the results of a dynamic light scattering study, which confirms the “pseudo-layer” structure of the TB phase with Beff in the range 10³–10⁴ Pa. We show additionally that the temperature dependence of Beff at the TB to nematic transition is accurately described by a coarse-grained free energy density, which is based on a Landau-deGennes expansion in terms of a heli-polar order parameter that characterizes the TB state and is linearly coupled to bend distortion of the director

Single-cell analysis of the 3D topologies of genomic loci using genome architecture mapping

Although each cell within an organism contains a nearly identical genome sequence, the three-dimensional (3D) packing of the genome varies among individual cells, influencing cell-type-specific gene expression. Genome Architecture Mapping (GAM) is the first genome-wide experimental method for capturing 3D proximities between any number of genomic loci without ligation. GAM overcomes several limitations of 3C-based methods by sequencing DNA from a large collection of thin sections sliced from individual nuclei. The GAM technique measures locus co-segregation, extracts radial positions, infers chromatin compaction, requires small numbers of cells, does not depend on ligation, and provides rich single-cell information. However, previous analyses of GAM data focused exclusively on population averages, neglecting the variation in 3D topology among individual cells. We present the first single-cell analysis of GAM data, demonstrating that the slices from individual cells reveal intercellular heterogeneity in chromosome conformation. By simultaneously clustering both slices and genomic loci, we identify topological variation among single cells, including differential compaction of cell cycle genes. We also develop a geometric model of the nucleus, allowing prediction of the 3D positions of each slice. Using GAM data from mouse embryonic stem cells, we make new discoveries about the structure of the major mammalian histone gene locus, which is incorporated into the Histone Locus Body (HLB), including structural fluctuations and putative causal molecular mechanisms. Our methods are packaged as SluiceBox, a toolkit for mining GAM data. Our approach represents a new method of investigating variation in 3D genome topology among individual cells across space and time