Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks

Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to capillaries and uses scaling exponents to quantify these changes. Prominent scaling theories predict that combinations of these exponents explain how metabolic, growth, and other biological rates vary with body size. Nevertheless, direct measurements of individual vessel segments have been limited because existing techniques for measuring vasculature are invasive, time consuming, and technically difficult. We developed software that extracts the length, radius, and connectivity of in vivo vessels from contrast-enhanced 3D Magnetic Resonance Angiography. Using data from 20 human subjects, we calculated scaling exponents by four methods--two derived from local properties of branching junctions and two from whole-network properties. Although these methods are often used interchangeably in the literature, we do not find general agreement between these methods, particularly for vessel lengths. Measurements for length of vessels also diverge from theoretical values, but those for radius show stronger agreement. Our results demonstrate that vascular network models cannot ignore certain complexities of real vascular systems and indicate the need to discover new principles regarding vessel lengths

On the Minimum Distance of Generalized Spatially Coupled LDPC Codes

Families of generalized spatially-coupled low-density parity-check (GSC-LDPC) code ensembles can be formed by terminating protograph-based generalized LDPC convolutional (GLDPCC) codes. It has previously been shown that ensembles of GSC-LDPC codes constructed from a protograph have better iterative decoding thresholds than their block code counterparts, and that, for large termination lengths, their thresholds coincide with the maximum a-posteriori (MAP) decoding threshold of the underlying generalized LDPC block code ensemble. Here we show that, in addition to their excellent iterative decoding thresholds, ensembles of GSC-LDPC codes are asymptotically good and have large minimum distance growth rates.Comment: Submitted to the IEEE International Symposium on Information Theory 201

Spatially Coupled LDPC Codes Constructed from Protographs

In this paper, we construct protograph-based spatially coupled low-density parity-check (SC-LDPC) codes by coupling together a series of L disjoint, or uncoupled, LDPC code Tanner graphs into a single coupled chain. By varying L, we obtain a flexible family of code ensembles with varying rates and frame lengths that can share the same encoding and decoding architecture for arbitrary L. We demonstrate that the resulting codes combine the best features of optimized irregular and regular codes in one design: capacity approaching iterative belief propagation (BP) decoding thresholds and linear growth of minimum distance with block length. In particular, we show that, for sufficiently large L, the BP thresholds on both the binary erasure channel (BEC) and the binary-input additive white Gaussian noise channel (AWGNC) saturate to a particular value significantly better than the BP decoding threshold and numerically indistinguishable from the optimal maximum a-posteriori (MAP) decoding threshold of the uncoupled LDPC code. When all variable nodes in the coupled chain have degree greater than two, asymptotically the error probability converges at least doubly exponentially with decoding iterations and we obtain sequences of asymptotically good LDPC codes with fast convergence rates and BP thresholds close to the Shannon limit. Further, the gap to capacity decreases as the density of the graph increases, opening up a new way to construct capacity achieving codes on memoryless binary-input symmetric-output (MBS) channels with low-complexity BP decoding.Comment: Submitted to the IEEE Transactions on Information Theor

Quasi-Cyclic Asymptotically Regular LDPC Codes

Families of "asymptotically regular" LDPC block code ensembles can be formed by terminating (J,K)-regular protograph-based LDPC convolutional codes. By varying the termination length, we obtain a large selection of LDPC block code ensembles with varying code rates, minimum distance that grows linearly with block length, and capacity approaching iterative decoding thresholds, despite the fact that the terminated ensembles are almost regular. In this paper, we investigate the properties of the quasi-cyclic (QC) members of such an ensemble. We show that an upper bound on the minimum Hamming distance of members of the QC sub-ensemble can be improved by careful choice of the component protographs used in the code construction. Further, we show that the upper bound on the minimum distance can be improved by using arrays of circulants in a graph cover of the protograph.Comment: To be presented at the 2010 IEEE Information Theory Workshop, Dublin, Irelan

New Codes on Graphs Constructed by Connecting Spatially Coupled Chains

A novel code construction based on spatially coupled low-density parity-check (SC-LDPC) codes is presented. The proposed code ensembles are described by protographs, comprised of several protograph-based chains characterizing individual SC-LDPC codes. We demonstrate that code ensembles obtained by connecting appropriately chosen SC-LDPC code chains at specific points have improved iterative decoding thresholds compared to those of single SC-LDPC coupled chains. In addition, it is shown that the improved decoding properties of the connected ensembles result in reduced decoding complexity required to achieve a specific bit error probability. The constructed ensembles are also asymptotically good, in the sense that the minimum distance grows linearly with the block length. Finally, we show that the improved asymptotic properties of the connected chain ensembles also translate into improved finite length performance.Comment: Submitted to IEEE Transactions on Information Theor

Conductivity phenomena in polycrystalline zinc oxide films

Photoconductivity and electric conductivity of polycrystalline zinc oxide thin film under low intensity irradiatio

Revisiting the observed surface climate response to large volcanic eruptions

In light of the range in presently available observational, reanalysis and model data, we revisit the surface climate response to large tropical volcanic eruptions from the end of the 19th century until present. We focus on the dynamically driven response of the North Atlantic Oscillation (NAO) and the radiative-driven tropical temperature response. Using 10 different reanalysis products and the Hadley Centre Sea Level Pressure observational dataset (HadSLP2) we confirm a positive tendency in the phase of the NAO during boreal winters following large volcanic eruptions, although we conclude that it is not as clear cut as the current literature suggests. While different reanalyses agree well on the sign of the surface volcanic NAO response for individual volcanoes, the spread in the response is often large (∼ 1/2 standard deviation). This inter-reanalysis spread is actually larger for the more recent volcanic eruptions, and in one case does not encompass observations (El Chichón). These are all in the satellite era and therefore assimilate more atmospheric data that may lead to a more complex interaction for the surface response. The phase of the NAO leads to a dynamically driven warm anomaly over northern Europe in winter, which is present in all datasets considered. The general cooling of the surface temperature due to reduced incoming shortwave radiation is therefore disturbed by dynamical impacts. In the tropics, where less dynamically driven influences are present, we confirm a predominant cooling after most but not all eruptions. All datasets agree well on the strength of the tropical response, with the observed and reanalysis response being statistically significant but the modelled response not being significant due to the high variability across models