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

Algebraic superposition of LDGM codes for cooperative diversity

Abstract-This paper presents a technique for achieving cooperative spatial diversity using serially concatenated low density generator matrix (LDGM) codes. Specifically, we consider a scenario in which a pair of transceivers employ algebraic superposition of error control codes to effect spatial diversity at their common destination. The construction of LDGM codes from a sparse generator matrix makes them a natural fit for such a cooperative diversity scheme. The simple decoder structure for graph based codes reduces the complexity at the destination compared with previously-proposed schemes using algebraic superposition of convolutional codes and turbo-like decoding. The result is a system with low encoding and decoding complexity and improved error performance

PDGF-C Induces Maturation of Blood Vessels in a Model of Glioblastoma and Attenuates the Response to Anti-VEGF Treatment

Recent clinical trials of VEGF inhibitors have shown promise in the treatment of recurrent glioblastomas (GBM). However, the survival benefit is usually short-lived as tumors escape anti-VEGF therapies. Here we tested the hypothesis that Platelet Derived Growth Factor-C (PDGF-C), an isoform of the PDGF family, affects GBM progression independent of VEGF pathway and hinders anti-VEGF therapy.We first showed that PDGF-C is present in human GBMs. Then, we overexpressed or downregulated PDGF-C in a human GBM cell line, U87MG, and grew them in cranial windows in nude mice to assess vessel structure and function using intravital microscopy. PDGF-C overexpressing tumors had smaller vessel diameters and lower vascular permeability compared to the parental or siRNA-transfected tumors. Furthermore, vessels in PDGF-C overexpressing tumors had more extensive coverage with NG2 positive perivascular cells and a thicker collagen IV basement membrane than the controls. Treatment with DC101, an anti-VEGFR-2 antibody, induced decreases in vessel density in the parental tumors, but had no effect on the PDGF-C overexpressing tumors.These results suggest that PDGF-C plays an important role in glioma vessel maturation and stabilization, and that it can attenuate the response to anti-VEGF therapy, potentially contributing to escape from vascular normalization

Probing the Functional Impact of Sequence Variation on p53-DNA Interactions Using a Novel Microsphere Assay for Protein-DNA Binding with Human Cell Extracts

The p53 tumor suppressor regulates its target genes through sequence-specific binding to DNA response elements (REs). Although numerous p53 REs are established, the thousands more identified by bioinformatics are not easily subjected to comparative functional evaluation. To examine the relationship between RE sequence variation—including polymorphisms—and p53 binding, we have developed a multiplex format microsphere assay of protein-DNA binding (MAPD) for p53 in nuclear extracts. Using MAPD we measured sequence-specific p53 binding of doxorubicin-activated or transiently expressed p53 to REs from established p53 target genes and p53 consensus REs. To assess the sensitivity and scalability of the assay, we tested 16 variants of the p21 target sequence and a 62-multiplex set of single nucleotide (nt) variants of the p53 consensus sequence and found many changes in p53 binding that are not captured by current computational binding models. A group of eight single nucleotide polymorphisms (SNPs) was examined and binding profiles closely matched transactivation capability tested in luciferase constructs. The in vitro binding characteristics of p53 in nuclear extracts recapitulated the cellular in vivo transactivation capabilities for eight well-established human REs measured by luciferase assay. Using a set of 26 bona fide REs, we observed distinct binding patterns characteristic of transiently expressed wild type and mutant p53s. This microsphere assay system utilizes biologically meaningful cell extracts in a multiplexed, quantitative, in vitro format that provides a powerful experimental tool for elucidating the functional impact of sequence polymorphism and protein variation on protein/DNA binding in transcriptional networks

Braided convolutional codes

We present a new class of iteratively decodable turbo-like codes, called braided convolutional codes. Constructions and encoding procedures for tightly and sparsely braided codes are introduced. Sparsely braided codes exhibit good convergence behavior with iterative decoding, and a statistical analysis using Markov permutors shows that the free distance of these codes grows linearly with constraint lengt