BAG : Managing GPU as buffer cache in operating systems

This paper presents the design, implementation and evaluation of BAG, a system that manages GPU as the buffer cache in operating systems. Unlike previous uses of GPUs, which have focused on the computational capabilities of GPUs, BAG is designed to explore a new dimension in managing GPUs in heterogeneous systems where the GPU memory is an exploitable but always ignored resource. With the carefully designed data structures and algorithms, such as concurrent hashtable, log-structured data store for the management of GPU memory, and highly-parallel GPU kernels for garbage collection, BAG achieves good performance under various workloads. In addition, leveraging the existing abstraction of the operating system not only makes the implementation of BAG non-intrusive, but also facilitates the system deployment

BAG: Managing GPU as Buffer Cache in Operating Systems

This paper presents the design, implementation and evaluation of BAG, a system that manages GPU as the buffer cache in operating systems. Unlike previous uses of GPUs, which have focused on the computational capabilities of GPUs, BAG is designed to explore a new dimension in managing GPUs in heterogeneous systems where the GPU memory is an exploitable but always ignored resource. With the carefully designed data structures and algorithms, such as concurrent hashtable, log-structured data store for the management of GPU memory, and highly-parallel GPU kernels for garbage collection, BAG achieves good performance under various workloads. In addition, leveraging the existing abstraction of the operating system not only makes the implementation of BAG non-intrusive, but also facilitates the system deployment

Evolution by gene duplication, recombination and selection in MHC class I genes of Odorrana margaretae

Amphibians have undergone catastrophic declines worldwide and the major histocompatibility complex (MHC) is an attractive candidate for investigating the link between adaptive variation and individual fitness. Nonetheless, little research has been conducted to study the amphibians MHC genes. Thus, MHC class Ia of Odorrana margaretae, a representative species of the Odorrana, was isolated and used to analyze the adaptive mechanism. We isolated alleles and determined evolution patterns of MHC class Ia in O. margaretae. The phylogenetic tree of MHC class Ia was reconstructed to understand the evolutionary relationship of Anura. In O. margaretae of MHC class Ia: there were more non-synonymous mutations compared to synonymous mutations; there are at least two loci; the recombination alleles took place for a large proportion (55.56%) of the alleles and recombination usually took place between whole exon of Ia genes of MHC class; positive selection sites were detected and most (10 of 19) located at the α1 and α2 domains belonged to the presumed ABS. The diversity of genes of MHC class Ia was led by recombination, gene duplication and positive selection. Trans-species polymorphisms of anuran genes of MHC class Ia were evident in anurans. Therefore, the MHC class Ia present demonstrative candidates for investigating the link between adaptive variation and individual fitness. We argue that knowledge of the MHC of other anuran lineage, especially focusing a genus such as O. margaretae, should provide an overall more complete picture of the organization of MHC in anurans

Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research

Background The rhesus macaque (RM, Macaca mulatta) is the most important nonhuman primate model in biomedical research. We present the first genomic survey of wild RMs, sequencing 81 geo-referenced individuals of five subspecies from 17 locations in China, a large fraction of the species’ natural distribution. Results Populations were structured into five genetic lineages on the mainland and Hainan Island, recapitulating current subspecies designations. These subspecies are estimated to have diverged 125.8 to 51.3 thousand years ago, but feature recent gene flow. Consistent with the expectation of a larger body size in colder climates and smaller body size in warmer climates (Bergman's rule), the northernmost RM lineage (M. m. tcheliensis), possessing the largest body size of all Chinese RMs, and the southernmost lineage (M. m. brevicaudus), with the smallest body size of all Chinese RMs, feature positively selected genes responsible for skeletal development. Further, two candidate selected genes (Fbp1, Fbp2) found in M. m. tcheliensis are involved in gluconeogenesis, potentially maintaining stable blood glucose levels during starvation when food resources are scarce in winter. The tropical subspecies M. m. brevicaudus showed positively selected genes related to cardiovascular function and response to temperature stimuli, potentially involved in tropical adaptation. We found 118 single-nucleotide polymorphisms matching human disease-causing variants with 82 being subspecies specific. Conclusions These data provide a resource for selection of RMs in biomedical experiments. The demographic history of Chinese RMs and their history of local adaption offer new insights into their evolution and provide valuable baseline information for biomedical investigation