A survey on architectures and energy efficiency in Data Center Networks

Data Center Networks (DCNs) are attracting growing interest from both academia and industry to keep pace with the exponential growth in cloud computing and enterprise networks. Modern DCNs are facing two main challenges of scalability and cost-effectiveness. The architecture of a DCN directly impacts on its scalability, while its cost is largely driven by its power consumption. In this paper, we conduct a detailed survey of the most recent advances and research activities in DCNs, with a special focus on the architectural evolution of DCNs and their energy efficiency. The paper provides a qualitative categorization of existing DCN architectures into switch-centric and server-centric topologies as well as their design technologies. Energy efficiency in data centers is discussed in details with survey of existing techniques in energy savings, green data centers and renewable energy approaches. Finally, we outline potential future research directions in DCNs

A Novel Secretory Poly-Cysteine and Histidine-Tailed Metalloprotein (Ts-PCHTP) from Trichinella spiralis (Nematoda)

BACKGROUND: Trichinella spiralis is an unusual parasitic intracellular nematode causing dedifferentiation of the host myofiber. Trichinella proteomic analyses have identified proteins that act at the interface between the parasite and the host and are probably important for the infection and pathogenesis. Many parasitic proteins, including a number of metalloproteins are unique for the nematodes and trichinellids and therefore present good targets for future therapeutic developments. Furthermore, detailed information on such proteins and their function in the nematode organism would provide better understanding of the parasite-host interactions. METHODOLOGY/PRINCIPAL FINDINGS: In this study we report the identification, biochemical characterization and localization of a novel poly-cysteine and histidine-tailed metalloprotein (Ts-PCHTP). The native Ts-PCHTP was purified from T. spiralis muscle larvae that were isolated from infected rats as a model system. The sequence analysis showed no homology with other proteins. Two unique poly-cysteine domains were found in the amino acid sequence of Ts-PCHTP. This protein is also the first reported natural histidine tailed protein. It was suggested that Ts-PCHTP has metal binding properties. Total Reflection X-ray Fluorescence (TXRF) assay revealed that it binds significant concentrations of iron, nickel and zinc at protein:metal ratio of about 1:2. Immunohistochemical analysis showed that the Ts-PCHTP is localized in the cuticle and in all tissues of the larvae, but that it is not excreted outside the parasite. CONCLUSIONS/SIGNIFICANCE: Our data suggest that Ts-PCHTP is the first described member of a novel nematode poly-cysteine protein family and its function could be metal storage and/or transport. Since this protein family is unique for parasites from Superfamily Trichinelloidea its potential applications in diagnostics and treatment could be exploited in future

An Agent-Based Model of a Hepatic Inflammatory Response to Salmonella: A Computational Study under a Large Set of Experimental Data

Citation: Shi, Z. Z., Chapes, S. K., Ben-Arieh, D., & Wu, C. H. (2016). An Agent-Based Model of a Hepatic Inflammatory Response to Salmonella: A Computational Study under a Large Set of Experimental Data. Plos One, 11(8), 39. doi:10.1371/journal.pone.0161131We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as "sepsis". Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-a ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies

Improving datacenter performance and robustness with multipath TCP

The latest large-scale data centers offer higher aggregate bandwidth and robustness by creating multiple paths in the core of the network. To utilize this bandwidth requires different flows take different paths, which poses a challenge. In short, a single-path transport seems ill-suited to such networks. We propose using Multipath TCP as a replacement for TCP in such data centers, as it can effectively and seamlessly use available bandwidth, giving improved throughput and better fairness on many topologies. We investigate what causes these benefits, teasing apart the contribution of each of the mechanisms used by MPTCP. Using MPTCP lets us rethink data center networks, with a different mindset as to the relationship between transport protocols, routing and topology. MPTCP enables topologies that single path TCP cannot utilize. As a proof-of-concept, we present a dual-homed variant of the FatTree topology. With MPTCP, this outperforms FatTree for a wide range of workloads, but costs the same. In existing data centers, MPTCP is readily deployable leveraging widely deployed technologies such as ECMP. We have run MPTCP on Amazon EC2 and found that it outperforms TCP by a factor of three when there is path diversity. But the biggest benefits will come when data centers are designed for multipath transports