Structured Random Linear Codes (SRLC): Bridging the Gap between Block and Convolutional Codes

Several types of AL-FEC (Application-Level FEC) codes for the Packet Erasure Channel exist. Random Linear Codes (RLC), where redundancy packets consist of random linear combinations of source packets over a certain finite field, are a simple yet efficient coding technique, for instance massively used for Network Coding applications. However the price to pay is a high encoding and decoding complexity, especially when working on $GF(2^8)$, which seriously limits the number of packets in the encoding window. On the opposite, structured block codes have been designed for situations where the set of source packets is known in advance, for instance with file transfer applications. Here the encoding and decoding complexity is controlled, even for huge block sizes, thanks to the sparse nature of the code and advanced decoding techniques that exploit this sparseness (e.g., Structured Gaussian Elimination). But their design also prevents their use in convolutional use-cases featuring an encoding window that slides over a continuous set of incoming packets. In this work we try to bridge the gap between these two code classes, bringing some structure to RLC codes in order to enlarge the use-cases where they can be efficiently used: in convolutional mode (as any RLC code), but also in block mode with either tiny, medium or large block sizes. We also demonstrate how to design compact signaling for these codes (for encoder/decoder synchronization), which is an essential practical aspect.Comment: 7 pages, 12 figure

Application Bat Algorithm for Estimating Super Pairwise Alignment Parameters on Similarity Analysis Between Virus Protein Sequences

There were many diseases caused by viruses or bacteria. the virus or bacteria can mutate so that they could result the new disease. Sequence alignment was important so that it could be used to research genetic diseases and epidemics. In this reseach, we took case study of dengue virus and zika virus. To see the similarity between original virus and the mutation virus, it wass required the alignment process of two virus sequences. The method used for aligning two virus sequences was Super Pairwise Alignment (SPA). Due to the similarity value depended on SPA parameters, in this research we would apply heuristic method, such as Bat Algorithm (BA) algorithm to optimize SPA parameters maximizing similarity value as objective function. BA was the optimization method which was inspired by the behavior of bats in using sonar called echolocation to detect prey, avoid obstacles. From the BA simulations, we could obtain optimal SPA parameters resulting maximum similarity value between two aligned each of dengue virus and zika virus protein sequences in approaching

Elucidating diversity in the class composition of the minicircle hypervariable region of Trypanosoma cruzi: New perspectives on typing and kDNA inheritance

Background Trypanosoma cruzi, the protozoan causative of Chagas disease, is classified into six main Discrete Typing Units (DTUs): TcI-TcVI. This parasite has around 105 copies of the minicircle hypervariable region (mHVR) in their kinetoplastic DNA (kDNA). The genetic diversity of the mHVR is virtually unknown. However, cross-hybridization assays using mHVRs showed hybridization only between isolates belonging to the same genetic group. Nowadays there is no methodologic approach with a good sensibility, specificity and reproducibility for direct typing on biological samples. Due to its high copy number and apparently high diversity, mHVR becomes a good target for typing. Methodology/Principal findings Around 22 million reads, obtained by amplicon sequencing of the mHVR, were analyzed for nine strains belonging to six T. cruzi DTUs. The number and diversity of mHVR clusters was variable among DTUs and even within a DTU. However, strains of the same DTU shared more mHVR clusters than strains of different DTUs and clustered together. In addition, hybrid DTUs (TcV and TcVI) shared similar percentages (1.9–3.4%) of mHVR clusters with their parentals (TcII and TcIII). Conversely, just 0.2% of clusters were shared between TcII and TcIII suggesting biparental inheritance of the kDNA in hybrids. Sequencing at low depth (20,000–40,000 reads) also revealed 95% of the mHVR clusters for each of the analyzed strains. Finally, the method revealed good correlation in cluster identity and abundance between different replications of the experiment (r = 0.999). Conclusions/Significance Our work sheds light on the sequence diversity of mHVRs at intra and inter-DTU level. The mHVR amplicon sequencing workflow described here is a reproducible technique, that allows multiplexed analysis of hundreds of strains and results promissory for direct typing on biological samples in a future. In addition, such approach may help to gain knowledge on the mechanisms of the minicircle evolution and phylogenetic relationships among strains.Fil: Tomasini, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; ArgentinaFil: Rusman, Fanny. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; ArgentinaFil: Floridia Yapur, Noelia Aldana del Rosario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; ArgentinaFil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Ragone, Paula Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; ArgentinaFil: Diosque, Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; Argentin

Robust QUIC: integrating practical coding in a low latency transport protocol

We introduce rQUIC, an integration of the QUIC protocol and a coding module. rQUIC has been designed to feature different coding/decoding schemes and is implemented in go language. We conducted an extensive measurement campaign to provide a thorough characterization of the proposed solution. We compared the performance of rQUIC with that of the original QUIC protocol for different underlying network conditions as well as different traffic patterns. Our results show that rQUIC not only yields a relevant performance gain (shorter delays), especially when network conditions worsen, but also ensures a more predictable behavior. For bulk transfer (long flows), the delay reduction almost reached 70% when the frame error rate was 5%, while under similar conditions, the gain for short flows (web navigation) was approximately 55%. In the case of video streaming, the QoE gain (p1203 metric) was, approximately, 50%.This work was supported in part by the Basque Government through the Elkartek Program under the Hodei-x Project under Agreement KK-2021/00049; in part by the Spanish Government through the Ministerio de Economía y Competitividad, Fondo Europeo de Desarrollo Regional (FEDER) through the Future Internet Enabled Resilient smart CitiEs (FIERCE) under Grant RTI2018-093475-AI00; and in part by the Industrial Doctorates Program of the University of Cantabria under Grant Call 2019

Aerodynamic Performance of a Biologically Inspired Hybrid Plasma-Mechanical Flow Control and Sensing Device

The continued high global demand for passenger and freight air traffic along with increased use of unmanned aerial vehicles operating in broader Reynolds number regimes has resulted in researchers examining alternative technologies, which would result in safer, more reliable, and superior performing aircraft. Aerodynamic flow control may be one of the most promising approaches to solving this problem, having already proven its ability to enable higher flow efficiency while simultaneously improving overall control of flow behavior such as laminar-to-turbulent transition. Recent research in aerodynamic flow control has seen a pronounced growth in the areas of biomimicry and plasma flow control actuators. Plasma actuators offer an inexpensive and energy efficient method of flow control. In addition, plasma actuator technology has the potential to be applied to a host of other aircraft performance parameters including applications in radar cross section mitigation and in situ wing deicing. Biomimetic researchers have studied large scale mechanics and phenomena such as flapping mechanics, and wing morphology, as well as small scale factors such as feather fluttering and microscale feather geometry. The proliferation of interest in these fields laid the foundation and inspiration for the development of a novel aerodynamic flow control and sensing device known as the compliant electrode discharge device, commonly referred to by the inventors as “plasma feathers”. This study consists of an investigation into the behavior of the compliant electrode device and its aerodynamic characteristics and performance during its flapping mode operation. Three models of varying aspect ratio were constructed, characterized through a modal analysis, and then subsequently tested for behavioral characteristic and aerodynamic performance. The behavioral testing shows that there is clearly defined range of pulsing ratios and duty cycle combinations that will likely result in desired behavior. The aerodynamic performance was investigated via two-dimensional two-component particle image velocimetry. It’s shown in tunnel-on testing that the device can favorably affect a low Reynolds number flow and potentially be used as an active airbrake in higher Reynolds number flows. Testing in quiescent air demonstrated that flows with velocities on the order of the speed of the tip of the compliant electrode can be induced in two momentum jets that are similar to the superposition of a traditional dielectric barrier discharges induced jet (horizontally oriented jet) and a synthetic jet’s induced jet (vertically oriented jet) overlayed upon one another allowing for a broad range of low Reynolds number applications