The free-living SAR11 clade is a globally abundant group of oceanic Alphaproteobacteria, with small genome sizes and rich genomic A+T content. However, the taxonomy of SAR11 has become controversial recently. Some researchers argue that the position of SAR11 is a sister group to Rickettsiales. Other researchers advocate that SAR11 is located within free-living lineages of Alphaproteobacteria. Here, we use the natural vector representation method to identify the evolutionary origin of the SAR11 clade. This alignment-free method does not depend on any model assumptions. With this approach, the correspondence between proteome sequences and their natural vectors is one-to-one. After fixing a set of proteins, each bacterium is represented by a set of vectors. The Hausdorff distance is then used to compute the dissimilarity distance between two bacteria. The phylogenetic tree can be reconstructed based on these distances. Using our method, we systematically analyze four data sets of alphaproteobacterial proteomes in order to reconstruct the phylogeny of Alphaproteobacteria. From this we can see that the phylogenetic position of the SAR11 group is within a group of other free-living lineages of Alphaproteobacteria.

Error reconciliation is an important technique for learning with error (LWE) and ring-LWE (RLWE)-based constructions. In this paper, we present a comparison analysis on two error reconciliation-based RLWE key exchange protocols: Ding et al. in 2012 (DING12) and Bos et al. in 2015 (BCNS15). We take them as examples to explain the core idea of error reconciliation, building key exchange over RLWE problem, implementation and real-world performance, and compare them comprehensively. We also analyse a LWE key exchange 'Frodo' that uses an improved error reconciliation mechanism in BCNS15. To the best of our knowledge, our work is the first to present at least 128-bit classic (80-bit quantum) and 256-bit classic (> 200-bit quantum) secure parameter choices for DING12 with efficient portable C/C++ implementations. Benchmark shows that our efficient implementation is 11× faster than BCNS15 and one key exchange execution only costs 0.07 ms on a four-year-old middle range CPU. Error reconciliation is 1.57× faster than BCNS15.

No abstract uploaded!

No abstract uploaded!

In the first part of this paper, we study Koszul property of directed graded categories. In the second part of this paper, we prove a general criterion for an infinite directed category to be Koszul. We show that infinite directed categories in the theory of representation stability are Koszul over a field of characteristic zero