Efficient Cache Coherence on Manycore Optical Networks

Ever since industry has turned to parallelism instead of frequency scaling to improve processor performance, multicore processors have continued to scale to larger and larger numbers of cores. Some believe that multicores will have 1000 cores or more by the middle of the next decade. However, their promise of increased performance will only be reached if their inherent scaling challenges are overcome. One such major scaling challenge is the viability of efficient cache coherence with large numbers of cores. Meanwhile, recent advances in nanophotonic device manufacturing are making CMOS-integrated optics a realityâ interconnect technology which can provide significantly more bandwidth at lower power than conventional electrical analogs. The contributions of this paper are two-fold. (1) It presents ATAC, a new manycore architecture that augments an electrical mesh network with an optical network that performs highly efficient broadcasts. (2) It introduces ACKwise, a novel directory-based cache coherence protocol that provides high performance and scalability on any large-scale manycore interconnection net- work with broadcast capability. Performance evaluation studies using analytical models show that (i) a 1024-core ATAC chip using ACKwise achieves a speedup of 3.9Ã compared to a similarly-sized pure electrical mesh manycore with a conventional limited directory protocol; (ii) the ATAC chip with ACKwise achieves a speedup of 1.35Ã compared to the electrical mesh chip with ACKwise; and (iii) a pure electrical mesh chip with ACKwise achieves a speedup of 2.9Ã over the same chip using a conventional limited directory protocol

Breast Cancer

This chapter in Cancer Concepts: A Guidebook for the Non-Oncologist presents an overview of breast cancer, including etiology, screening, pathology, staging, and treatment.https://escholarship.umassmed.edu/cancer_concepts/1019/thumbnail.jp

Colorectal Cancer

This chapter in Cancer Concepts: A Guidebook for the Non-Oncologist presents an overview of colorectal cancer, including etiology, screening, pathology, staging, and treatment.https://escholarship.umassmed.edu/cancer_concepts/1015/thumbnail.jp

A New Biophysical Metric for Interrogating the Information Content in Human Genome Sequence Variation: Proof of Concept

Various studies have shown an association between single nucleotide polymorphisms (SNPs) and common disease. We hypothesize that information encoded in the structure of SNP haploblock variation illumines molecular pathways and cellular mechanisms involved in the regulation of host adaptation to the environment. We developed and utilized the normalized information content (NIC), a novel metric based on SNP haploblock variation. We found that all SNP haploblocks with statistically low information content contained putative transcription factor binding sites and microRNA motifs. We were able to translate a biophysical, mathematical measure of common variants into a deeper understanding of the life sciences through analysis of biochemical patterns associated with SNP haploblock variation. We submit that this new metric, NIC, may be useful in decoding the functional significance of common variation in the human genome and in analyzing the regulation of molecular pathways involved in host adaptation to environmental pathogens.Comment: 13 page

Rapid detection of BRCA1/2 recurrent mutations in Chinese breast and ovarian cancer patients with multiplex SNaPshot genotyping panels.

BRCA1/2 mutations are significant risk factors for hereditary breast and ovarian cancer (HBOC), its mutation frequency in HBOC of Chinese ethnicity is around 9%, in which nearly half are recurrent mutations. In Hong Kong and China, genetic testing and counseling are not as common as in the West. To reduce the barrier of testing, a multiplex SNaPshot genotyping panel that targeted 25 Chinese BRCA1/2 mutation hotspots was developed, and its feasibility was evaluated in a local cohort of 441 breast and 155 ovarian cancer patients. For those who tested negative, they were then subjected to full-gene testing with next-generation sequencing (NGS). BRCA mutation prevalence in this cohort was 8.05% and the yield of the recurrent panel was 3.52%, identifying over 40% of the mutation carriers. Moreover, from 79 Chinese breast cancer cases recruited overseas, 2 recurrent mutations and one novel BRCA2 mutation were detected by the panel and NGS respectively. The developed genotyping panel showed to be an easy-to-perform and more affordable testing tool that can provide important contributions to improve the healthcare of Chinese women with cancer as well as family members that harbor high risk mutations for HBOC

Assessment of myofascial pain syndrome among married female healthcare workers: a cross sectional comparative study in a tertiary care centre

Background: Myofascial pain syndrome (MPS) is common among females between ages 20-40 years. Psychosomatic and mechanical reasons are attributed as causative factors. Female health care workers (FHW) in hospitals with rapid patient turn over are vulnerable to develop MPS. Our aim was to ascertain the prevalence of MPS in married FHW working in various departments of the hospital and its association with poor sleep and work stress. Methods: We selected married FHWs in 20-50 years age group and divided them into two groups, medical and paramedical (those involved directly and indirectly with patient care respectively). MPS was diagnosed after detailed personal interview and clinical examination. Sleep duration was divided into less than 5 hours and more than 5hours. Presence of work-related stress and other medical parameters were also recorded. Results: A total of 150 medical and 150 paramedical FHWs were included in the study. Overall prevalence of MPS among FHWs was 42%, of which, medical group was 32% and paramedical was 52%. The paramedical group showed significantly higher prevalence of MPS (p: 0.02). Sleep was less than 5 hours in 29.3% of medical FHW and 13.3% of paramedical. This difference didn’t show any association to MPS (p=0.8). 38% FHW perceived excessive work stress, 40% were paramedical and 36% were medical. This didn’t correlate with prevalence of MPS (p=0.2) among them. Conclusions: Paramedical FHW experienced more MPS than medical and it was more of mechanical type and not due to work stress or sleep deprivation

Eddy properties in the California Current System

Eddy detection and tracking algorithms are applied to both satellite altimetry and a high‐resolution (dx = 5 km) climatological model solution of the U.S. West Coast to study the properties of surface and undercurrent eddies in the California Current System. Eddy properties show remarkable similarity in space and time, and even somewhat in polarity. Summer and fall are the most active seasons for undercurrent eddy generation, while there is less seasonal variation at surface. Most of the eddies have radii in the range of 25–100 km, sea level anomaly amplitudes of 1–4 cm, and vorticity normalized by ƒ amplitudes of 0.025–0.2. Many of the eddies formed near the coast travel considerable distance westward with speeds about 2 km/day, consistent with the β effect. Anticyclones and cyclones show equatorward and poleward displacements, respectively. Long‐lived surface eddies show a cyclonic dominance. The subsurface California Undercurrent generates more long‐lived anticyclones than cyclones through instabilities and topographic/coastline effects. In contrast, surface eddies and subsurface cyclones have much more widely distributed birth sites. The majority of the identified eddies have lifetimes less than a season. Eddies extend to 800–1500 m depth and have distinctive vertical structures for cyclones and anticyclones. Eddies show high nonlinearity (rotation speed higher than propagation speed) and hence can be efficient in transporting materials offshore