Array Convolutional Low-Density Parity-Check Codes

This paper presents a design technique for obtaining regular time-invariant low-density parity-check convolutional (RTI-LDPCC) codes with low complexity and good performance. We start from previous approaches which unwrap a low-density parity-check (LDPC) block code into an RTI-LDPCC code, and we obtain a new method to design RTI-LDPCC codes with better performance and shorter constraint length. Differently from previous techniques, we start the design from an array LDPC block code. We show that, for codes with high rate, a performance gain and a reduction in the constraint length are achieved with respect to previous proposals. Additionally, an increase in the minimum distance is observed.Comment: 4 pages, 2 figures, accepted for publication in IEEE Communications Letter

Progressive Differences Convolutional Low-Density Parity-Check Codes

We present a new family of low-density parity-check (LDPC) convolutional codes that can be designed using ordered sets of progressive differences. We study their properties and define a subset of codes in this class that have some desirable features, such as fixed minimum distance and Tanner graphs without short cycles. The design approach we propose ensures that these properties are guaranteed independently of the code rate. This makes these codes of interest in many practical applications, particularly when high rate codes are needed for saving bandwidth. We provide some examples of coded transmission schemes exploiting this new class of codes.Comment: 8 pages, 2 figures. Accepted for publication in IEEE Communications Letters. Copyright transferred to IEE

Time-Invariant Spatially Coupled Low-Density Parity-Check Codes with Small Constraint Length

We consider a special family of SC-LDPC codes, that is, time-invariant LDPCC codes, which are known in the literature for a long time. Codes of this kind are usually designed by starting from QC block codes, and applying suitable unwrapping procedures. We show that, by directly designing the LDPCC code syndrome former matrix without the constraints of the underlying QC block code, it is possible to achieve smaller constraint lengths with respect to the best solutions available in the literature. We also find theoretical lower bounds on the syndrome former constraint length for codes with a specified minimum length of the local cycles in their Tanner graphs. For this purpose, we exploit a new approach based on a numerical representation of the syndrome former matrix, which generalizes over a technique we already used to study a special subclass of the codes here considered.Comment: 5 pages, 4 figures, to be presented at IEEE BlackSeaCom 201

Personal genome editing algorithms to identify increased variant-induced off-target potential

Clustered regularly interspaced short palindromic repeats (CRISPR) technologies allow for facile genomic modification in a site-specific manner. A key step in this process is the in-silico design of single guide RNAs (sgRNAs) to efficiently and specifically target a site of interest. To this end, it is necessary to enumerate all potential off-target sites within a given genome that could be inadvertently altered by nuclease-mediated cleavage. Off-target sites are quasi-complementary regions of the genome in which the specified sgRNA can bind, even without a perfect complementary nucleotides sequence. This problem is known as off-target sites enumeration and became common after discovery of CRISPR technology. To solve this problem, many in-silico solutions were proposed in the last years but, currently available software for this task are limited by computational efficiency, variant support, genetic annotation, assessment of the functional impact of potential off-target effects at population and individual level, and a user-friendly graphical interface designed to be usable by non-informatician without any programming knowledge. This thesis addresses all these topics by proposing two software to directly answer the off-target enumeration problem and perform all the related analysis. In details, the thesis proposes CRISPRitz, a tool designed and developed to compute fast and exhaustive searches on reference and alternative genome to enumerate all the possible off-target for a user-defined set of sgRNAs with specific thresholds of mismatches (non-complementary bps in RNA-DNA binding) and bulges (bubbles that alters the physical structure of RNA and DNA limiting the binding activity). The thesis also proposes CRISPRme, a tool developed starting from CRISPRitz, which answers the requests of professionals and technicians to implement a comprehensive and easy to use interface to perform off-target enumeration, analysis and assessment, with graphical reports, a graphical interface and the capability of performing real-time query on the resulting data to extract desired targets, with a focus on individual and personalized genome analysis

Building scalable digital library ingestion pipelines using microservices

CORE, a harvesting service offering access to millions of open access research papers from around the world, has shifted its harvesting process from following a monolithic approach to the adoption of a microservices infrastructure. In this paper, we explain how we rearranged and re-scheduled our old ingestion pipeline, present CORE's move to managing microservices and outline the tools we use in a new and optimised ingestion system. In addition, we discuss the ineffciencies of our old harvesting process, the advantages, and challenges of our new ingestion system and our future plans. We conclude that via the adoption of microservices architecture we managed to achieve a scalable and distributed system that would assist with CORE's future performance and evolution

Design and Analysis of Time-Invariant SC-LDPC Convolutional Codes With Small Constraint Length

In this paper, we deal with time-invariant spatially coupled low-density parity-check convolutional codes (SC-LDPC-CCs). Classic design approaches usually start from quasi-cyclic low-density parity-check (QC-LDPC) block codes and exploit suitable unwrapping procedures to obtain SC-LDPC-CCs. We show that the direct design of the SC-LDPC-CCs syndrome former matrix or, equivalently, the symbolic parity-check matrix, leads to codes with smaller syndrome former constraint lengths with respect to the best solutions available in the literature. We provide theoretical lower bounds on the syndrome former constraint length for the most relevant families of SC-LDPC-CCs, under constraints on the minimum length of cycles in their Tanner graphs. We also propose new code design techniques that approach or achieve such theoretical limits.Comment: 30 pages, 5 figures, accepted for publication in IEEE Transactions on Communication

Three-dimensional dispersion induced by extreme tensile strain in La_(2–x)Sr_xCuO_4 films

The electronic band structure probed by angle-resolved photoemission spectroscopy on thin epitaxial La2–xSrxCuO4 films under extreme tensile strain shows anomalous features compatible with c-axis dispersion. This result is in striking contrast with the usual quasi-two-dimensional (2D) dispersion observed up to now in most superconducting cuprates, including relaxed and compressively strained La2–xSrxCuO4 films grown under the same conditions. The data were analyzed using a 3D tight-binding dispersion for a body-centered-tetragonal lattice. We relate the enhancement of the c-axis dispersion to the significant displacement of the apical oxygen induced by epitaxial strain

Punctured Binary Simplex Codes as LDPC codes

Digital data transfer can be protected by means of suitable error correcting codes. Among the families of state-of-the-art codes, LDPC (Low Density Parity-Check) codes have received a great deal of attention recently, because of their performance and flexibility of operation, in wireless and mobile radio channels, as well as in cable transmission systems. In this paper, we present a class of rate-adaptive LDPC codes, obtained as properly punctured simplex codes. These codes allow for the use of an efficient soft-decision decoding algorithm, provided that a condition called row-column constraint is satisfied. This condition is tested on small-length codes, and then extended to medium-length codes. The puncturing operations we apply do not influence the satisfaction of the row-column constraint, assuring that a wide range of code rates can be obtained. We can reach code rates remarkably higher than those obtainable by the original simplex code, and the price in terms of minimum distance turns out to be relatively small, leading to interesting trade-offs in the resulting asymptotic coding gain