Rhymes: a shared virtual memory system for non-coherent tiled many-core architectures

The rising core count per processor is pushing chip complexity to a level that hardware-based cache coherency protocols become too hard and costly to scale. We need new designs of many-core hardware and software other than traditional technologies to keep up with the ever-increasing scalability demands. The Intel Single-chip Cloud Computer (SCC) is a recent research processor exemplifying a new cluster-on-chip architecture which promotes a software-oriented approach instead of hardware support to implementing shared memory coherence. This paper presents a shared virtual memory (SVM) system, dubbed Rhymes, tailored to such a new processor kind of non-coherent and hybrid memory architectures. Rhymes features a two-way cache coherence protocol to enforce release consistency for pages allocated in shared physical memory (SPM) and scope consistency for pages in per-core private memory. It also supports page remapping on a per-core basis to boost data locality. We implement Rhymes on the SCC port of the Barrelfish OS. Experimental results show that our SVM outperforms the pure SPM approach used by Intel's software managed coherence (SMC) library by up to 12 times, with superlinear speedups (due to L2 cache effect) noted for applications with strong data reuse patterns.published_or_final_versio

High hepatitis B surface antigen levels predict insignificant fibrosis in hepatitis B e antigen positive chronic hepatitis B

INTRODUCTION: There is no data on the relationship between hepatitis B surface antigen (HBsAg) levels and liver fibrosis in hepatitis B e antigen (HBeAg)-positive patients with chronic hepatitis B (CHB). METHODS: Serum HBsAg and HBV DNA levels in HBeAg-positive CHB patients with liver biopsies were analyzed. The upper limit of normal (ULN) of alanine aminotransferase (ALT) was 30 and 19 U/L for men and women respectively. Histologic assessment was based on Ishak fibrosis staging for fibrosis and Knodell histologic activity index (HAI) for necroinflammation. RESULTS: 140 patients (65% male, median age 32.7 years) were recruited. 56 (40%) had ALT 1, had significantly higher median HBsAg levels (50,320 and 7,820 IU/mL respectively, p/= 25,000 IU/mL was independently associated with fibrosis score </= 1 (p=0.025, odds ratio 9.042).Using this cut-off HBsAg level in patients with ALT </=2xULN, positive and negative predictive values for predicting fibrosis score </= 1 were 92.7% and 60.0% respectively. HBV DNA levels had no association with liver histology. CONCLUSION: Among HBeAg-positive patients with ALT </=2xULN, high serum HBsAg levels can accurately predict fibrosis score </= 1, and could potentially influence decisions concerning treatment commencement and reduce the need for liver biopsy.published_or_final_versio

What drives the evolution of gas kinematics in star-forming galaxies?

One important result from recent large integral field spectrograph (IFS) surveys is that the intrinsic velocity dispersion of galaxies traced by star-forming gas increases with redshift. Massive, rotation-dominated discs are already in place at z ∼ 2, but they are dynamically hotter than spiral galaxies in the local Universe. Although several plausible mechanisms for this elevated velocity dispersion (e.g. star formation feedback, elevated gas supply, or more frequent galaxy interactions) have been proposed, the fundamental driver of the velocity dispersion enhancement at high redshift remains unclear. We investigate the origin of this kinematic evolution using a suite of cosmological simulations from the FIRE (Feedback In Realistic Environments) project. Although IFS surveys generally cover a wider range of stellar masses than in these simulations, the simulated galaxies show trends between intrinsic velocity dispersion (σ intr ), SFR, and z in agreement with observations. In both observations and simulations, galaxies on the star-forming main sequence have median σ intr values that increase from z ∼ 0 to z ∼ 1–1.5, but this increasing trend is less evident at higher redshift. In the FIRE simulations, σ intr can vary significantly on time-scales of 100 Myr. These variations closely mirror the time evolution of the SFR and gas inflow rate (M gas ). By cross-correlating pairs of σ intr, M gas, and SFR, we show that increased gas inflow leads to subsequent enhanced star formation, and enhancements in σ intr tend to temporally coincide with increases in M gas and SFR

Artificial neural network accurately predicts hepatitis B surface antigen seroclearance

BACKGROUND & AIMS: Hepatitis B surface antigen (HBsAg) seroclearance and seroconversion are regarded as favorable outcomes of chronic hepatitis B (CHB). This study aimed to develop artificial neural networks (ANNs) that could accurately predict HBsAg seroclearance or seroconversion on the basis of available serum variables. METHODS: Data from 203 untreated, HBeAg-negative CHB patients with spontaneous HBsAg seroclearance (63 with HBsAg seroconversion), and 203 age- and sex-matched HBeAg-negative controls were analyzed. ANNs and logistic regression models (LRMs) were built and tested according to HBsAg seroclearance and seroconversion. Predictive accuracy was assessed with area under the receiver operating characteristic curve (AUROC). RESULTS: Serum quantitative HBsAg (qHBsAg) and HBV DNA levels, qHBsAg and HBV DNA reduction were related to HBsAg seroclearance (P<0.001) and were used for ANN/LRM-HBsAg seroclearance building, whereas, qHBsAg reduction was not associated with ANN-HBsAg seroconversion (P = 0.197) and LRM-HBsAg seroconversion was solely based on qHBsAg (P = 0.01). For HBsAg seroclearance, AUROCs of ANN were 0.96, 0.93 and 0.95 for the training, testing and genotype B subgroups respectively. They were significantly higher than those of LRM, qHBsAg and HBV DNA (all P<0.05). Although the performance of ANN-HBsAg seroconversion (AUROC 0.757) was inferior to that for HBsAg seroclearance, it tended to be better than those of LRM, qHBsAg and HBV DNA. CONCLUSIONS: ANN identifies spontaneous HBsAg seroclearance in HBeAg-negative CHB patients with better accuracy, on the basis of easily available serum data. More useful predictors for HBsAg seroconversion are still needed to be explored in the future.published_or_final_versio

Identification of Hepatitis B Virus DNA Polymerase Sequences to Predict Virological Response to Entecavir Therapy

Poster Presentations: Emerging / Infectious DiseasesConference Theme: Translating Health Research into Policy and Practice for Health of the Populationpublished_or_final_versio

Risk Factors and Post-Resection Independent Predictive Score for the Recurrence of Hepatitis B-Related Hepatocellular Carcinoma

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Boundary entropy of supersymmetric Janus solutions

In this paper we compute the holographic boundary entropy for half-BPS Janus deformations of the $AdS_3\times S^3\times T^4$ vacuum of type IIB supergravity. Previous work \cite{Chiodaroli:2009yw} has shown that there are two independent deformations of this sort. In one case, the six-dimensional dilaton jumps across the interface, while the other case displays a jump of axion and four-form potential. In case of a jump of the six-dimensional dilaton, it is possible to compare the holographic result with the weak-coupling result for a two-dimensional interface CFT where the radii of the compactified bosons jump across the interface. We find exact agreement between holographic and CFT results. This is to be contrasted with the holographic calculation for the non-supersymmetric Janus solution, which agrees with the CFT result only at the leading order in the jump parameter. We also examine the implications of the holographic calculation in case of a solution with a jump in the axion, which can be associated with a deformation of the CFT by the $Z_2$-orbifold twist operator.Comment: 35 pages, pdf-LaTeX, 5 figures, v2: minor changes, typos corrected, reference adde

Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations

Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth

Prevalence of occult hepatitis B infection in a highly endemic area for chronic hepatitis B: A study of a large blood donor population

Background and aims: The aim of the present study was to determine the population prevalence of occult hepatitis B (OHB) infection and its clinical profile in a highly endemic area of chronic hepatitis B virus disease. Methods: OHB was first identified by individual sample testing for hepatitis B surface antigen (HBsAg) followed by nucleic acid testing (NAT) and vice versa for 3044 (cohort 1, stored sera from donation within 1 year) and 9990 (cohort 2, prospective study) blood donors, respectively. OHB was confirmed meticulously by ≥2 out of 3 tests with detectable hepatitis B virus (HBV) DNA using a sensitive standardised assay. Detailed serology and viral load in the serum and liver were studied. Results: The prevalence of OHB was 0.13% (4/3044) and 0.11% (11/9967) for cohort 1 and 2, respectively. In cohort 2, 10 out of 11 OHB samples were positive for anti-HBc (hepatitis B core antigen) antibody (all were immunoglobulin G). Seven had detectable anti-HBs. The serum HBV DNA levels were extremely low (highest 14.1 IU/ml). Of the six donors who underwent liver biopsies, all had normal liver biochemistry, extremely low liver HBV DNA (highest 6.21 copies/cell) and nearly normal liver histology. For those with viral sequence generation, none had the common HBsAg mutant G145R. Conclusions: The prevalence of OHB in a highly endemic area of chronic HBV was very low, thus implying a low impact on transfusion services. To implement universal screening, the high cost of NAT should be taken into account. OHB blood donors had very low HBV replication, and normal liver biochemistry and histology, conferring a favourable prognosis.published_or_final_versio