Deriving Good LDPC Convolutional Codes from LDPC Block Codes

Low-density parity-check (LDPC) convolutional codes are capable of achieving excellent performance with low encoding and decoding complexity. In this paper we discuss several graph-cover-based methods for deriving families of time-invariant and time-varying LDPC convolutional codes from LDPC block codes and show how earlier proposed LDPC convolutional code constructions can be presented within this framework. Some of the constructed convolutional codes significantly outperform the underlying LDPC block codes. We investigate some possible reasons for this "convolutional gain," and we also discuss the --- mostly moderate --- decoder cost increase that is incurred by going from LDPC block to LDPC convolutional codes.Comment: Submitted to IEEE Transactions on Information Theory, April 2010; revised August 2010, revised November 2010 (essentially final version). (Besides many small changes, the first and second revised versions contain corrected entries in Tables I and II.

Exact Free Distance and Trapping Set Growth Rates for LDPC Convolutional Codes

Ensembles of (J,K)-regular low-density parity-check convolutional (LDPCC) codes are known to be asymptotically good, in the sense that the minimum free distance grows linearly with the constraint length. In this paper, we use a protograph-based analysis of terminated LDPCC codes to obtain an upper bound on the free distance growth rate of ensembles of periodically time-varying LDPCC codes. This bound is compared to a lower bound and evaluated numerically. It is found that, for a sufficiently large period, the bounds coincide. This approach is then extended to obtain bounds on the trapping set numbers, which define the size of the smallest, non-empty trapping sets, for these asymptotically good, periodically time-varying LDPCC code ensembles.Comment: To be presented at the 2011 IEEE International Symposium on Information Theor

Gender equality and investments in adolescents in the rural Philippines:

"...Many studies have looked at the way resources are distributed to men, women, and especially to small children, but one age group within the family has been largely ignored: the adolescents. Adolescence is a crucial period in that teenagers can make major contributions to their families' welfare through their labor and earnings, in and outside the household, but may sacrifice their own wishes and future well-being in the process if such contributions come at the expense of investments in their education. The research methodology in this report, combining regression analysis with ethnography, provides a lesson in how complementarities between methodological approaches can be exploited...The research finds that parents are not unduly influenced by short-term needs and are ready to make substantial sacrifices in terms of current consumption in order to invest in their children's future. The research also concludes that boys and girls in this rural area of the Philippines are generally treated equally, provid ing a contrast with other Asian settings where discrimination by gender is common." (Forward by Per Pinstrup- Andersen)Teenagers Philippines Social conditions., Rural families Philippines., Gender, Health and nutrition, Education Economic aspects Philippines., Household resource allocation, Health.,

Threshold Analysis of Non-Binary Spatially-Coupled LDPC Codes with Windowed Decoding

In this paper we study the iterative decoding threshold performance of non-binary spatially-coupled low-density parity-check (NB-SC-LDPC) code ensembles for both the binary erasure channel (BEC) and the binary-input additive white Gaussian noise channel (BIAWGNC), with particular emphasis on windowed decoding (WD). We consider both (2,4)-regular and (3,6)-regular NB-SC-LDPC code ensembles constructed using protographs and compute their thresholds using protograph versions of NB density evolution and NB extrinsic information transfer analysis. For these code ensembles, we show that WD of NB-SC-LDPC codes, which provides a significant decrease in latency and complexity compared to decoding across the entire parity-check matrix, results in a negligible decrease in the near-capacity performance for a sufficiently large window size W on both the BEC and the BIAWGNC. Also, we show that NB-SC-LDPC code ensembles exhibit gains in the WD threshold compared to the corresponding block code ensembles decoded across the entire parity-check matrix, and that the gains increase as the finite field size q increases. Moreover, from the viewpoint of decoding complexity, we see that (3,6)-regular NB-SC-LDPC codes are particularly attractive due to the fact that they achieve near-capacity thresholds even for small q and W.Comment: 6 pages, 8 figures; submitted to 2014 IEEE International Symposium on Information Theor

Giardia Cyst Wall Protein 1 Is a Lectin That Binds to Curled Fibrils of the GalNAc Homopolymer

The infectious and diagnostic stage of Giardia lamblia (also known as G. intestinalis or G. duodenalis) is the cyst. The Giardia cyst wall contains fibrils of a unique β-1,3-linked N-acetylgalactosamine (GalNAc) homopolymer and at least three cyst wall proteins (CWPs) composed of Leu-rich repeats (CWPLRR) and a C-terminal conserved Cys-rich region (CWPCRR). Our goals were to dissect the structure of the cyst wall and determine how it is disrupted during excystation. The intact Giardia cyst wall is thin (~400 nm), easily fractured by sonication, and impermeable to small molecules. Curled fibrils of the GalNAc homopolymer are restricted to a narrow plane and are coated with linear arrays of oval-shaped protein complex. In contrast, cyst walls of Giardia treated with hot alkali to deproteinate fibrils of the GalNAc homopolymer are thick (~1.2 µm), resistant to sonication, and permeable. The deproteinated GalNAc homopolymer, which forms a loose lattice of curled fibrils, is bound by native CWP1 and CWP2, as well as by maltose-binding protein (MBP)-fusions containing the full-length CWP1 or CWP1LRR. In contrast, neither MBP alone nor MBP fused to CWP1CRR bind to the GalNAc homopolymer. Recombinant CWP1 binds to the GalNAc homopolymer within secretory vesicles of Giardia encysting in vitro. Fibrils of the GalNAc homopolymer are exposed during excystation or by treatment of heat-killed cysts with chymotrypsin, while deproteinated fibrils of the GalNAc homopolymer are degraded by extracts of Giardia cysts but not trophozoites. These results show the Leu-rich repeat domain of CWP1 is a lectin that binds to curled fibrils of the GalNAc homopolymer. During excystation, host and Giardia proteases appear to degrade bound CWPs, exposing fibrils of the GalNAc homopolymer that are digested by a stage-specific glycohydrolase. Author SummaryWhile the walls of plants and fungi contain numerous sugar homopolymers (cellulose, chitin, and β-1,3-glucans) and dozens of proteins, the cyst wall of Giardia is relatively simple. The Giardia wall contains a unique homopolymer of β-1,3-linked N-acetylgalactosamine (GalNAc) and at least three cyst wall proteins (CWPs), each of which is composed of Leu-rich repeats and a C-terminal Cys-rich region. The three major discoveries here are: 1) Fibrils of the GalNAc homopolymer are curled and form a lattice that is compressed into a narrow plane by bound protein in intact cyst walls. 2) Leu-rich repeats of CWP1 form a novel lectin domain that is specific for fibrils of the GalNAc homopolymer, which can be isolated by methods used to deproteinate fungal walls. 3) A cyst-specific glycohydrolase is able to degrade deproteinated fibrils of the GalNAc homopolymer. We incorporate these findings into a new curled fiber and lectin model of the intact Giardia cyst wall and a protease and glycohydrolase model of excystation.National Institutes of Health (AI048082, AI44070, GM31318, RR1088

Exposure-Lag-Response in Longitudinal Studies: Application of Distributed-Lag Nonlinear Models in an Occupational Cohort.

Prolonged exposures can have complex relationships with health outcomes, as timing, duration, and intensity of exposure are all potentially relevant. Summary measures such as cumulative exposure or average intensity of exposure may not fully capture these relationships. We applied penalized and unpenalized distributed-lag nonlinear models (DLNMs) with flexible exposure-response and lag-response functions in order to examine the association between crystalline silica exposure and mortality from lung cancer and nonmalignant respiratory disease in a cohort study of 2,342 California diatomaceous earth workers followed during 1942-2011. We also assessed associations using simple measures of cumulative exposure assuming linear exposure-response and constant lag-response. Measures of association from DLNMs were generally higher than those from simpler models. Rate ratios from penalized DLNMs corresponding to average daily exposures of 0.4 mg/m3 during lag years 31-50 prior to the age of observed cases were 1.47 (95% confidence interval (CI): 0.92, 2.35) for lung cancer mortality and 1.80 (95% CI: 1.14, 2.85) for nonmalignant respiratory disease mortality. Rate ratios from the simpler models for the same exposure scenario were 1.15 (95% CI: 0.89, 1.48) and 1.23 (95% CI: 1.03, 1.46), respectively. Longitudinal cohort studies of prolonged exposures and chronic health outcomes should explore methods allowing for flexibility and nonlinearities in the exposure-lag-response

The glucocorticoid-Angptl4-ceramide axis induces insulin resistance through PP2A and PKCζ.

Chronic glucocorticoid exposure is associated with the development of insulin resistance. We showed that glucocorticoid-induced insulin resistance was attenuated upon ablation of Angptl4, a glucocorticoid target gene encoding the secreted protein angiopoietin-like 4, which mediates glucocorticoid-induced lipolysis in white adipose tissue. Through metabolomic profiling, we revealed that glucocorticoid treatment increased hepatic ceramide concentrations by inducing enzymes in the ceramide synthetic pathway in an Angptl4-dependent manner. Angptl4 was also required for glucocorticoids to stimulate the activities of the downstream effectors of ceramide, protein phosphatase 2A (PP2A) and protein kinase Cζ (PKCζ). We further showed that knockdown of PP2A or inhibition of PKCζ or ceramide synthesis prevented glucocorticoid-induced glucose intolerance in wild-type mice. Moreover, the inhibition of PKCζ or ceramide synthesis did not further improve glucose tolerance in Angptl4-/- mice, suggesting that these molecules were major downstream effectors of Angptl4. Overall, our study demonstrates the key role of Angptl4 in glucocorticoid-augmented hepatic ceramide production that induces whole-body insulin resistance

Randomly Punctured LDPC Codes

In this paper, we present a random puncturing analysis of low-density parity-check (LDPC) code ensembles. We derive a simple analytic expression for the iterative belief propagation (BP) decoding threshold of a randomly punctured LDPC code ensemble on the binary erasure channel (BEC) and show that, with respect to the BP threshold, the strength and suitability of an LDPC code ensemble for random puncturing is completely determined by a single constant that depends only on the rate and the BP threshold of the mother code ensemble. We then provide an efficient way to accurately predict BP thresholds of randomly punctured LDPC code ensembles on the binary- input additive white Gaussian noise channel (BI-AWGNC), given only the BP threshold of the mother code ensemble on the BEC and the design rate, and we show how the prediction can be improved with knowledge of the BI-AWGNC threshold. We also perform an asymptotic minimum distance analysis of randomly punctured code ensembles and present simulation results that confirm the robust decoding performance promised by the asymptotic results. Protograph-based LDPC block code and spatially coupled LDPC code ensembles are used throughout as examples to demonstrate the results