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Creators/Authors contains: "Lin, Xing"

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  1. null (Ed.)
  2. Abstract Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, ‘Brockarchaeota’, named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling. 
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  3. Data deduplication has been widely used in storage systems to improve storage efficiency and I/O performance. In particular, content-defined variable-size chunking (CDC) is often used in data deduplication systems for its capability to detect and remove duplicate data in modified files. However, the CDC algorithm is very compute-intensive and inherently sequential. Efforts on accelerating it by segmenting a file and running the algorithm independently on each segment in parallel come at a cost of substantial degradation of deduplication ratio. In this paper, we propose SS-CDC, a two-stage parallel CDC, that enables (almost) full parallelism on chunking of a file without compromising deduplication ratio. Further, SS-CDC exploits instruction-level SIMD parallelism available in today's processors. As a case study, by using Intel AVX-512 instructions, SS-CDC consistently obtains superlinear speedups on a multi-core server. Our experiments using real-world datasets show that, compared to existing parallel CDC methods which only achieve up to a 7.7X speedup on an 8-core processor with the deduplication ratio degraded by up to 40%, SS-CDC can achieve up to a 25.6X speedup with no loss of deduplication ratio. 
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