Network-error correcting codes using small fields

Recently, Ebrahimi and Fragouli proposed an algorithm to construct scalar network codes using small fields (and vector network codes of small lengths) satisfying multicast constraints in a given single-source, acyclic network. The contribution of this paper is two fold. Primarily, we extend the scalar network coding algorithm of Ebrahimi and Fragouli (henceforth referred to as the EF algorithm) to block network-error correction. Existing construction algorithms of block network-error correcting codes require a rather large field size, which grows with the size of the network and the number of sinks, and thereby can be prohibitive in large networks. We give an algorithm which, starting from a given network-error correcting code, can obtain another network code using a small field, with the same error correcting capability as the original code. Our secondary contribution is to improve the EF Algorithm itself. The major step in the EF algorithm is to find a least degree irreducible polynomial which is coprime to another large degree polynomial. We suggest an alternate method to compute this coprime polynomial, which is faster than the brute force method in the work of Ebrahimi and Fragouli.

A cyclic peptide mimic of an RNA recognition motif of human La protein is a potent inhibitor of hepatitis C virus

Due to limited available therapeutic options, developing new lead compounds against hepatitis C virus is an urgent need. Human La protein stimulates hepatitis C virus translation through interaction with the hepatitis C viral RNA. A cyclic peptide mimicking the beta-turn of the human La protein that interacts with the viral RNA was synthesized. It inhibits hepatitis C viral RNA translation significantly better than the corresponding linear peptide at longer post-treatment times. The cyclic peptide also inhibited replication as measured by replicon RNA levels using real time RT-PCR. The cyclic peptide emerges as a promising lead compound against hepatitis C.

Performance improvement of short-length regular low-density parity-check codes with low-complexity post-processing

It is well known that extremely long low-density parity-check (LDPC) codes perform exceptionally well for error correction applications, short-length codes are preferable in practical applications. However, short-length LDPC codes suffer from performance degradation owing to graph-based impairments such as short cycles, trapping sets and stopping sets and so on in the bipartite graph of the LDPC matrix. In particular, performance degradation at moderate to high E-b/N-0 is caused by the oscillations in bit node a posteriori probabilities induced by short cycles and trapping sets in bipartite graphs. In this study, a computationally efficient algorithm is proposed to improve the performance of short-length LDPC codes at moderate to high E-b/N-0. This algorithm makes use of the information generated by the belief propagation (BP) algorithm in previous iterations before a decoding failure occurs. Using this information, a reliability-based estimation is performed on each bit node to supplement the BP algorithm. The proposed algorithm gives an appreciable coding gain as compared with BP decoding for LDPC codes of a code rate equal to or less than 1/2 rate coding. The coding gains are modest to significant in the case of optimised (for bipartite graph conditioning) regular LDPC codes, whereas the coding gains are huge in the case of unoptimised codes. Hence, this algorithm is useful for relaxing some stringent constraints on the graphical structure of the LDPC code and for developing hardware-friendly designs.

The precision with which single cells of Dictyostelium discoideum can locate a source of cyclic AMP

When stimulated by a point source of cyclic AMP, a starved amoeba of Dictyostelium discoideum responds by putting out a hollow balloon-like membrane extension followed by a pseudopod. The effect of the stimulus is to influence the position where either of these protrusions is made on the cell rather than to cause them to be made. Because the pseudopod forms perpendicular to the cell surface, its location is a measure of the precision with which the cell can locate the cAMP source. Cells beyond 1 h of starvation respond non-randomly with a precision that improves steadily thereafter. A cell that is starved for 1-2 h can locate the source accurately 43% of the time; and if starved for 6-7 h, 87% of the time. The response always has a high scatter; population-level heterogeneity reflects stochasticity in single cell behaviour. From the angular distribution of the response its maximum information content is estimated to be 2-3 bits. In summary, we quantitatively demonstrate the stochastic nature of the directional response and the increase in its accuracy over time.

Cyclic AMP-dependent protein lysine acylation in mycobacteria regulates fatty acid and propionate metabolism

Acetylation of lysine residues is a posttranslational modification that is used by both eukaryotes and prokaryotes to regulate a variety of biological processes. Here we identify multiple substrates for the cAMP-dependent protein lysine acetyltransferase from Mycobacterium tuberculosis (KATmt). We demonstrate that a catalytically important lysine residue in a number of FadD (fatty acyl CoA synthetase) enzymes is acetylated by KATmt in a cAMP-dependent manner and that acetylation inhibits the activity of FadD enzymes. A sirtuin-like enzyme can deacetylate multiple FadDs, thus completing the regulatory cycle. Using a strain deleted for the KATmt ortholog in Mycobacterium bovis Bacillus Calmette-Guerin (BCG), we show for the first time that acetylation is dependent on intracellular cAMP levels. KATmt can utilize propionyl CoA as a substrate and, therefore, plays a critical role in alleviating propionyl CoA toxicity in mycobacteria by inactivating acyl CoA synthetase (ACS). The precision by which mycobacteria can regulate the metabolism of fatty acids in a cAMP-dependent manner appears to be unparalleled in other biological organisms and is ideally suited to adapt to the complex environment that pathogenic mycobacteria experience in the host.

Cyclic nucleotide signaling in intestinal epithelia: getting to the gut of the matter

The intestine is the primary site of nutrient absorption, fluid-ion secretion, and home to trillions of symbiotic microbiota. The high turnover of the intestinal epithelia also renders it susceptible to neoplastic growth. These diverse processes are carefully regulated by an intricate signaling network. Among the myriad molecules involved in intestinal epithelial cell homeostasis are the second messengers, cyclic AMP (cAMP) and cyclic GMP (cGMP). These cyclic nucleotides are synthesized by nucleotidyl cyclases whose activities are regulated by extrinsic and intrinsic cues. Downstream effectors of cAMP and cGMP include protein kinases, cyclic nucleotide gated ion channels, and transcription factors, which modulate key processes such as ion-balance, immune response, and cell proliferation. The web of interaction involving the major signaling pathways of cAMP and cGMP in the intestinal epithelial cell, and possible cross-talk among the pathways, are highlighted in this review. Deregulation of these pathways occurs during infection by pathogens, intestinal inflammation, and cancer. Thus, an appreciation of the importance of cyclic nucleotide signaling in the intestine furthers our understanding of bowel disease, thereby aiding in the development of therapeutic approaches.

Codes with local regeneration

Regenerating codes and codes with locality are schemes recently proposed for a distributed storage network. While regenerating codes minimize the data downloaded for node repair, codes with locality minimize the number of nodes accessed during repair. In this paper, we provide some constructions of codes with locality, in which the local codes are regenerating codes, thereby combining the advantages of both classes of codes. The proposed constructions achieve an upper bound on minimum distance and are hence optimal. The constructions include both the cases when the local regenerating codes correspond to the MSR point as well as the MBR point on the storage repair-bandwidth tradeoff curve.

Cyclic AMP in Mycobacteria: the second messenger comes first

Cyclic AMP (cAMP) has emerged as a pivotal molecule for signalling in all life forms. Mycobacterial genomes have been found to encode for numerous proteins that are involved in cAMP generation, degradation and utilization. Many of these proteins have domain organizations unique to mycobacteria. This review summarizes recent advances in mechanisms of cAMP synthesis and degradation, focusing on the processes by which cAMP modulates mycobacterial signalling. We explore its impact on the physiology of the organism and on the discourse between M. tuberculosis and its host.

Better QOS with W/T SPR codes for the transmission of multimedia signals in Optical CDMA networks

In this paper optical code-division multiple-access (O-CDMA) packet network is considered, which offers inherent security in the access networks. The application of O-CDMA to multimedia transmission (voice, data, and video) is investigated. The simultaneous transmission of various services is achieved by assigning to each user unique multiple code signatures. Thus, by applying a parallel mapping technique, we achieve multi-rate services. A random access protocol is proposed, here, where all distinct codes are used, for packet transmission. The codes, Optical Orthogonal Code (OOC), or 1D codes and Wavelength/Time Single-Pulse-per-Row (W/T SPR), or 2D codes, are analyzed. These 1D and 2D codes with varied weight are used to differentiate the Quality of Service (QoS). The theoretical bit error probability corresponding to the quality of each service is established using 1D and 2D codes in the receiver noiseless case and compared. The results show that, using 2D codes QoS in multimedia transmission is better than using 1D codes.

Generalized distributive law for ML decoding of STBCs: further results

The problem of designing good Space-Time Block Codes (STBCs) with low maximum-likelihood (ML) decoding complexity has gathered much attention in the literature. All the known low ML decoding complexity techniques utilize the same approach of exploiting either the multigroup decodable or the fast-decodable (conditionally multigroup decodable) structure of a code. We refer to this well known technique of decoding STBCs as Conditional ML (CML) decoding. In [1], we introduced a framework to construct ML decoders for STBCs based on the Generalized Distributive Law (GDL) and the Factor-graph based Sum-Product Algorithm, and showed that for two specific families of STBCs, the Toepltiz codes and the Overlapped Alamouti Codes (OACs), the GDL based ML decoders have strictly less complexity than the CML decoders. In this paper, we introduce a `traceback' step to the GDL decoding algorithm of STBCs, which enables roughly 4 times reduction in the complexity of the GDL decoders proposed in [1]. Utilizing this complexity reduction from `traceback', we then show that for any STBC (not just the Toeplitz and Overlapped Alamouti Codes), the GDL decoding complexity is strictly less than the CML decoding complexity. For instance, for any STBC obtained from Cyclic Division Algebras that is not multigroup or conditionally multigroup decodable, the GDL decoder provides approximately 12 times reduction in complexity compared to the CML decoder. Similarly, for the Golden code, which is conditionally multigroup decodable, the GDL decoder is only about half as complex as the CML decoder.

A matroidal framework for network-error correcting codes

Matroidal networks were introduced by Dougherty et al. and have been well studied in the recent past. It was shown that a network has a scalar linear network coding solution if and only if it is matroidal associated with a representable matroid. The current work attempts to establish a connection between matroid theory and network-error correcting codes. In a similar vein to the theory connecting matroids and network coding, we abstract the essential aspects of network-error correcting codes to arrive at the definition of a matroidal error correcting network. An acyclic network (with arbitrary sink demands) is then shown to possess a scalar linear error correcting network code if and only if it is a matroidal error correcting network associated with a representable matroid. Therefore, constructing such network-error correcting codes implies the construction of certain representable matroids that satisfy some special conditions, and vice versa.

Construction of Block Orthogonal STBCs and Reducing Their Sphere Decoding Complexity

Construction of high rate Space Time Block Codes (STBCs) with low decoding complexity has been studied widely using techniques such as sphere decoding and non Maximum-Likelihood (ML) decoders such as the QR decomposition decoder with M paths (QRDM decoder). Recently Ren et al., presented a new class of STBCs known as the block orthogonal STBCs (BOSTBCs), which could be exploited by the QRDM decoders to achieve significant decoding complexity reduction without performance loss. The block orthogonal property of the codes constructed was however only shown via simulations. In this paper, we give analytical proofs for the block orthogonal structure of various existing codes in literature including the codes constructed in the paper by Ren et al. We show that codes formed as the sum of Clifford Unitary Weight Designs (CUWDs) or Coordinate Interleaved Orthogonal Designs (CIODs) exhibit block orthogonal structure. We also provide new construction of block orthogonal codes from Cyclic Division Algebras (CDAs) and Crossed-Product Algebras (CPAs). In addition, we show how the block orthogonal property of the STBCs can be exploited to reduce the decoding complexity of a sphere decoder using a depth first search approach. Simulation results of the decoding complexity show a 30% reduction in the number of floating point operations (FLOPS) of BOSTBCs as compared to STBCs without the block orthogonal structure.

Regenerating codes for errors and erasures in distributed storage

Regenerating codes are a class of codes proposed for providing reliability of data and efficient repair of failed nodes in distributed storage systems. In this paper, we address the fundamental problem of handling errors and erasures at the nodes or links, during the data-reconstruction and node-repair operations. We provide explicit regenerating codes that are resilient to errors and erasures, and show that these codes are optimal with respect to storage and bandwidth requirements. As a special case, we also establish the capacity of a class of distributed storage systems in the presence of malicious adversaries. While our code constructions are based on previously constructed Product-Matrix codes, we also provide necessary and sufficient conditions for introducing resilience in any regenerating code.

Generalization of deviated linear cyclic pursuit

Earlier work on cyclic pursuit systems has shown that using heterogeneous gains for agents in linear cyclic pursuit, the point of convergence (rendezvous point) can be chosen arbitrarily. But there are some restrictions on this set of reachable points. The use of deviated cyclic pursuit, as discussed in this paper, expands this set of reachable points to include points which are not reachable by any known linear cyclic pursuit scheme. The limits on the deviations are determined by stability considerations. Such limits have been analytically obtained in this paper along with results on the expansion in reachable set and the latter has also been verified through simulations.

Codes for solving three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces

Three codes, that can solve three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces, are provided here. The file 'bemconst.m' contains a MATLAB code for solving three dimensional linear elastostatic problems using constant boundary elements while ignoring body forces. The file 'bemconst.f90' is a Fortran translation of the MATLAB code contained in the file 'bemconst.m'. The file 'bemconstp.f90' is a parallelized version of the Fortran code contained in the file 'bemconst.f90'. The file 'inbem96.txt' is the input file for the Fortran codes contained in the files 'bemconst.f90' and 'bemconstp.f90'. Author hereby declares that the present codes are the original works of the author. Further, author hereby declares that any of the present codes, in full or in part, is not a translation or a copy of any of the existing codes written by someone else. Author's institution (Indian Institute of Science) has informed the author in writing that the institution is not interested in claiming any copyright on the present codes. Author is hereby distributing the present codes under the MIT License; full text of the license is included in each of the files that contain the codes.