Enhancing design space exploration by extending CPU/GPU specifications onto FPGAs

The design cycle for complex special-purpose computing systems is extremely costly and time-consuming. It involves a multiparametric design space exploration for optimization, followed by design verification. Designers of special purpose VLSI implementations often need to explore parameters, such as optimal bitwidth and data representation, through time-consuming Monte Carlo simulations. A prominent example of this simulation-based exploration process is the design of decoders for error correcting systems, such as the Low-Density Parity-Check (LDPC) codes adopted by modern communication standards, which involves thousands of Monte Carlo runs for each design point. Currently, high-performance computing offers a wide set of acceleration options that range from multicore CPUs to Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs). The exploitation of diverse target architectures is typically associated with developing multiple code versions, often using distinct programming paradigms. In this context, we evaluate the concept of retargeting a single OpenCL program to multiple platforms, thereby significantly reducing design time. A single OpenCL-based parallel kernel is used without modifications or code tuning on multicore CPUs, GPUs, and FPGAs. We use SOpenCL (Silicon to OpenCL), a tool that automatically converts OpenCL kernels to RTL in order to introduce FPGAs as a potential platform to efficiently execute simulations coded in OpenCL. We use LDPC decoding simulations as a case study. Experimental results were obtained by testing a variety of regular and irregular LDPC codes that range from short/medium (e.g., 8,000 bit) to long length (e.g., 64,800 bit) DVB-S2 codes. We observe that, depending on the design parameters to be simulated, on the dimension and phase of the design, the GPU or FPGA may suit different purposes more conveniently, thus providing different acceleration factors over conventional multicore CPUs.

Viscosity Control for Extrusion Processes Using Recycled Polymers

The aim of this paper is to develop a new extruder control system for recycled materials which has ability to automatically maintain constant a polymer melt viscosity of mixed recycled polymers during extrusion, regardless of variations in the Melt Flow Index (MFI) of recycled mixed grade high density polyethylene (HDPE) feedstock. A closed-loop controller is developed to automatically regulate screw speed and barrel temperature profile to achieve constant viscosity and enable consistent processing of variable grade recycled HDPE materials. The experimental results of real time viscosity measurement and control using a 38mm single screw extruder with different recycled HDPEs with widely different MFIs are reported in this work

FRENKEL-KONTOROVA DOMAIN-WALL PHASE-TRANSITIONS IN AN ADSORBED LAYER - POTASSIUM ON CO(10(1)OVER-BAR-0)

As the potassium fractional coverage of a cobalt {1010BAR} surface is increased over the range 0.2 to 0.6 monolayer the adlayer passes through a series of phase transitions. A commensurate phase is formed at exactly 0.5 monolayer, and corresponds to adatoms bonded in high-symmetry hollow sites on the unreconstructed cobalt surface, with an effective adatom radius lying between the ionic and covalent radii of potassium. A detailed structural study shows that the structural transitions can be characterised within a one-dimensional Frenkel-Kontorova model, with small lateral displacements of adatoms away from hollow sites in the low and high coverage phases. The low coverage phases progress from a distributed vacancy structure to a low density domain-wall structure; while the high coverage phase formed above half a monolayer is a high density asymmetric domain-wall structure.

Processability, structural evolution and properties of melt processed biaxially stretched HDPE/MWCNT nanocomposites

Biaxial stretching of melt mixed high density polyethylene (HDPE)/multiwalled carbon nanotube (MWCNT) nanocomposites was conducted in the melt state at different stretching ratios (SRs). The addition of MWCNTs leads to significant strain hardening in the HDPE, greatly improving the stability and thus processability of the stretching process. Scanning electron microscopy shows that the MWCNTs in the polymer matrix are gradually disentangled and randomly oriented in the stretching plane with increasing SRs. All the stretched samples exhibit an increase in crystallinity (about 10%) due to strain induced crystallization and a broadened distribution of crystallite size according to the XRD and DSC results. The mechanical properties of the composites improve with increasing SRs, while they drop off after a SR of 2.5 for the neat HDPE which is likely to be due to the relaxation of polymer chains prior to solidification. The presence of the MWCNTs appears to inhibit this relaxation thus helping to maintain the orientation and mechanical properties at high SRs. The modulus, yield strength and breaking strength of stretched composites with 8 wt% MWCNTs increase by approximately 54%, 85% and 193% respectively compared with the neat HDPE at a SR of 3. The electrical percolation threshold for the unstretched material occurs at 1.9 wt% MWCNTs. As SR increases, the values of critical concentration increase from 1.9 wt% to 4.9 wt% implying the destruction of conductive networks due to an increased inter-particle distance. A loading of 6 wt% MWCNTs is sufficient to ensure that the sheet conductivity is robust to changes in the SR. Decreased values of critical exponent from 1.9 to 1.1 and morphological investigation reveal a transformation of the system structure from three dimensional to two dimensional as SR increases.

The effect of melt viscosity on thermal efficiency for single screw extrusion of HDPE

In this work, a highly instrumented single screw extruder has been used to study the effect of polymer rheology on the thermal efficiency of the extrusion process. Three different molecular weight grades of high density polyethylene (HDPE) were extruded at a range of conditions. Three geometries of extruder screws were used at several set temperatures and screw rotation speeds. The extruder was equipped with real-time quantification of energy consumption; thermal dynamics of the process were examined using thermocouple grid sensors at the entrance to the die. Results showed that polymer rheology had a significant effect on process energy consumption and thermal homogeneity of the melt. Highest specific energy consumption and poorest homogeneity was observed for the highest viscosity grade of HDPE. Extruder screw geometry, set extrusion temperature and screw rotation speed were also found to have a direct effect on energy consumption and melt consistency. In particular, specific energy consumption was lower using a barrier flighted screw compared to single flighted screws at the same set conditions. These results highlight the complex nature of extrusion thermal dynamics and provide evidence that rheological properties of the polymer can significantly influence the thermal efficiency of the process.

Effect of high temperature, biaxial stretching on the thermal and mechanical properties of HDPE/MWCNT sheet

High density polyethylene (HDPE)/multi-walled carbon nanotube (MWCNT) composites containing 4 wt% MWCNTs were prepared by melt mixing followed by compression moulding into sheet. Compression moulded sheets were heated to just below the melting temperature and biaxially stretched at ratios (SRs) of 2, 2.5 and 3.0. The effect of stretching on the thermal and mechanical properties of the sheet was studied by differential scanning calorimetry (DSC) and tensile testing. DSC results show that the crystallinity of all the stretched samples increases by approximately 13% due to strain induced crystallization. The melting temperature of the biaxially stretched samples increases only slightly while crystallization temperature is not affected. Tensile test results indicate that at a SR of 2.5 the elastic modulus of the stretched composites increases by 17.6% relative to the virgin HDPE, but the breaking strength decreases by 33%. While the elastic modulus and breaking strength of the HDPE/MWCNT samples continue to increase as SR increases they drop off after a SR of 2.5 for the virgin HDPE. This is probably due to the constraining influence of the nanotubes preventing the relaxation of polymer chains caused by adiabatic heating at high SRs. The addition of MWCNTs results in significant strain hardening during deformation. While this will lead to increased energy requirement in forming it will also result in a more stable process and the ability to produce deep draw containers with more uniform wall thickness

Gene expression and epigenetic discovery screen reveal methylation of SFRP2 in prostate cancer

Aberrant activation of Wnts is common in human cancers, including prostate. Hypermethylation associated transcriptional silencing of Wnt antagonist genes SFRPs (Secreted Frizzled-Related Proteins) is a frequent oncogenic event. The significance of this is not known in prostate cancer. The objectives of our study were to (i) profile Wnt signaling related gene expression and (ii) investigate methylation of Wnt antagonist genes in prostate cancer. Using TaqMan Low Density Arrays, we identified 15 Wnt signaling related genes with significantly altered expression in prostate cancer; the majority of which were upregulated in tumors. Notably, histologically benign tissue from men with prostate cancer appeared more similar to tumor (r = 0.76) than to benign prostatic hyperplasia (BPH; r = 0.57, p < 0.001). Overall, the expression profile was highly similar between tumors of high (≥ 7) and low (≤ 6) Gleason scores. Pharmacological demethylation of PC-3 cells with 5-Aza-CdR reactivated 39 genes (≥ 2-fold); 40% of which inhibit Wnt signaling. Methylation frequencies in prostate cancer were 10% (2/20) (SFRP1), 64.86% (48/74) (SFRP2), 0% (0/20) (SFRP4) and 60% (12/20) (SFRP5). SFRP2 methylation was detected at significantly lower frequencies in high-grade prostatic intraepithelial neoplasia (HGPIN; 30%, (6/20), p = 0.0096), tumor adjacent benign areas (8.82%, (7/69), p < 0.0001) and BPH (11.43% (4/35), p < 0.0001). The quantitative level of SFRP2 methylation (normalized index of methylation) was also significantly higher in tumors (116) than in the other samples (HGPIN = 7.45, HB = 0.47, and BPH = 0.12). We show that SFRP2 hypermethylation is a common event in prostate cancer. SFRP2 methylation in combination with other epigenetic markers may be a useful biomarker of prostate cancer.

Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms

Epidemiological studies suggest a relationship between blood lipids and immune-mediated diseases, but the nature of these associations is not well understood. We used genome-wide association studies (GWAS) to investigate shared single nucleotide polymorphisms (SNPs) between blood lipids and immune-mediated diseases. We analyzed data from GWAS (n~200,000 individuals), applying new False Discovery Rate (FDR) methods, to investigate genetic overlap between blood lipid levels [triglycerides (TG), low density lipoproteins (LDL), high density lipoproteins (HDL)] and a selection of archetypal immune-mediated diseases (Crohn's disease, ulcerative colitis, rheumatoid arthritis, type 1 diabetes, celiac disease, psoriasis and sarcoidosis). We found significant polygenic pleiotropy between the blood lipids and all the investigated immune-mediated diseases. We discovered several shared risk loci between the immune-mediated diseases and TG (n = 88), LDL (n = 87) and HDL (n = 52). Three-way analyses differentiated the pattern of pleiotropy among the immune-mediated diseases. The new pleiotropic loci increased the number of functional gene network nodes representing blood lipid loci by 40%. Pathway analyses implicated several novel shared mechanisms for immune pathogenesis and lipid biology, including glycosphingolipid synthesis (e.g. FUT2) and intestinal host-microbe interactions (e.g. ATG16L1). We demonstrate a shared genetic basis for blood lipids and immune-mediated diseases independent of environmental factors. Our findings provide novel mechanistic insights into dyslipidemia and immune-mediated diseases and may have implications for therapeutic trials involving lipid-lowering and anti-inflammatory agents.

Shared common variants in prostate cancer and blood lipids

BACKGROUND: Epidemiological and clinical studies suggest comorbidity between prostate cancer (PCA) and cardiovascular disease (CVD) risk factors. However, the relationship between these two phenotypes is still not well understood. Here we sought to identify shared genetic loci between PCA and CVD risk factors.

METHODS: We applied a genetic epidemiology method based on conjunction false discovery rate (FDR) that combines summary statistics from different genome-wide association studies (GWAS), and allows identification of genetic overlap between two phenotypes. We evaluated summary statistics from large, multi-centre GWA studies of PCA (n=50 000) and CVD risk factors (n=200 000) [triglycerides (TG), low-density lipoprotein (LDL) cholesterol and high-density lipoprotein (HDL) cholesterol, systolic blood pressure, body mass index, waist-hip ratio and type 2 diabetes (T2D)]. Enrichment of single nucleotide polymorphisms (SNPs) associated with PCA and CVD risk factors was assessed with conditional quantile-quantile plots and the Anderson-Darling test. Moreover, we pinpointed shared loci using conjunction FDR.

RESULTS: We found the strongest enrichment of P-values in PCA was conditional on LDL and conditional on TG. In contrast, we found only weak enrichment conditional on HDL or conditional on the other traits investigated. Conjunction FDR identified altogether 17 loci; 10 loci were associated with PCA and LDL, 3 loci were associated with PCA and TG and additionally 4 loci were associated with PCA, LDL and TG jointly (conjunction FDR <0.01). For T2D, we detected one locus adjacent to HNF1B.

CONCLUSIONS: We found polygenic overlap between PCA predisposition and blood lipids, in particular LDL and TG, and identified 17 pleiotropic gene loci between PCA and LDL, and PCA and TG, respectively. These findings provide novel pathobiological insights and may have implications for trials using targeting lipid-lowering agents in a prevention or cancer setting.

Wnt signaling in age-related macular degeneration: human macular tissue and mouse model

BACKGROUND: The wingless-type MMTV integration site (Wnt) signaling is a group of signal transduction pathways. In canonical Wnt pathway, Wnt ligands bind to low-density lipoprotein receptor-related protein 5 or 6 (LRP5 or LRP6), resulting in phosphorylation and activation of the receptor. We hypothesize that canonical Wnt pathway plays a role in the retinal lesion of age-related macular degeneration (AMD), a leading cause of irreversible central visual loss in elderly.

METHODS: We examined LRP6 phosphorylation and Wnt signaling cascade in human retinal sections and plasma kallistatin, an endogenous inhibitor of the Wnt pathway in AMD patients and non-AMD subjects. We also used the Ccl2 (-/-) /Cx3cr1 (-/-) /rd8 and Ccl2 (-/-) /Cx3cr1 (gfp/gfp) mouse models with AMD-like retinal degeneration to further explore the involvement of Wnt signaling activation in the retinal lesions in those models and to preclinically evaluate the role of Wnt signaling suppression as a potential therapeutic option for AMD.

RESULTS: We found higher levels of LRP6 (a key Wnt signaling receptor) protein phosphorylation and transcripts of the Wnt pathway-targeted genes, as well as higher beta-catenin protein in AMD macula compared to controls. Kallistatin was decreased in the plasma of AMD patients. Retinal non-phosphorylated-β-catenin and phosphorylated-LRP6 were higher in Ccl2 (-/-) /Cx3cr1 (-/-) /rd8 mice than that in wild type. Intravitreal administration of an anti-LRP6 antibody slowed the progression of retinal lesions in Ccl2 (-/-) /Cx3cr1 (-/-) /rd8 and Ccl2 (-/-) /Cx3cr1 (gfp/gfp) mice. Electroretinography of treated eyes exhibited larger amplitudes compared to controls in both mouse models. A2E, a retinoid byproduct associated with AMD was lower in the treated eyes of Ccl2 (-/-) /Cx3cr1 (-/-) /rd8 mice. Anti-LRP6 also suppressed the expression of Tnf-α and Icam-1 in Ccl2 (-/-) /Cx3cr1 (-/-) /rd8 retinas.

CONCLUSIONS: Wnt signaling may be disturbed in AMD patients, which could contribute to the retinal inflammation and increased A2E levels found in AMD. Aberrant activation of canonical Wnt signaling might also contribute to the focal retinal degenerative lesions of mouse models with Ccl2 and Cx3cr1 deficiency, and intravitreal administration of anti-LRP6 antibody could be beneficial by deactivating the canonical Wnt pathway.

Genetically Determined Height and Coronary Artery Disease

Background: The nature and underlying mechanisms of an inverse association between adult height and the risk of coronary artery disease (CAD) are unclear. 
Methods: We used a genetic approach to investigate the association between height and CAD, using 180 height-associated genetic variants. We tested the association between a change in genetically determined height of 1 SD (6.5 cm) with the risk of CAD in 65,066 cases and 128,383 controls. Using individual-level genotype data from 18,249 persons, we also examined the risk of CAD associated with the presence of various numbers of height-associated alleles. To identify putative mechanisms, we analyzed whether genetically determined height was associated with known cardiovascular risk factors and performed a pathway analysis of the height-associated genes. 
Results: We observed a relative increase of 13.5% (95% confidence interval [CI], 5.4 to 22.1; P<0.001) in the risk of CAD per 1-SD decrease in genetically determined height. There was a graded relationship between the presence of an increased number of height-raising variants and a reduced risk of CAD (odds ratio for height quartile 4 versus quartile 1, 0.74; 95% CI, 0.68 to 0.84; P<0.001). Of the 12 risk factors that we studied, we observed significant associations only with levels of low-density lipoprotein cholesterol and triglycerides (accounting for approximately 30% of the association). We identified several overlapping pathways involving genes associated with both development and atherosclerosis. 
Conclusions: There is a primary association between a genetically determined shorter height and an increased risk of CAD, a link that is partly explained by the association between shorter height and an adverse lipid profile. Shared biologic processes that determine achieved height and the development of atherosclerosis may explain some of the association. (Funded by the British Heart Foundation and others.)

Refresh-free dynamic standard-cell based memories: Application to a QC-LDPC decoder

The area and power consumption of low-density parity check (LDPC) decoders are typically dominated by embedded memories. To alleviate such high memory costs, this paper exploits the fact that all internal memories of a LDPC decoder are frequently updated with new data. These unique memory access statistics are taken advantage of by replacing all static standard-cell based memories (SCMs) of a prior-art LDPC decoder implementation by dynamic SCMs (D-SCMs), which are designed to retain data just long enough to guarantee reliable operation. The use of D-SCMs leads to a 44% reduction in silicon area of the LDPC decoder compared to the use of static SCMs. The low-power LDPC decoder architecture with refresh-free D-SCMs was implemented in a 90nm CMOS process, and silicon measurements show full functionality and an information bit throughput of up to 600 Mbps (as required by the IEEE 802.11n standard).

Home-range size in juveniles of the temperate reef fish, the common triplefin (Forsterygion lapillum)

An organism’s home range dictates the spatial scale on which important processes occur (e.g. competition and predation) and directly affects the relationship between individual fitness and local habitat quality. Many reef fish species have very restricted home ranges after settlement and, here, we quantify home-range size in juveniles of a widespread and abundant reef fish in New Zealand, the common triplefin (Forsterygion lapillum). We conducted visual observations on 49 juveniles (mean size = 35-mm total length) within the Wellington harbour, New Zealand. Home ranges were extremely small, 0.053 m2 ± 0.029 (mean ± s.d.) and were unaffected by adult density, body size or substrate composition. A regression tree indicated that home-range size sharply decreased ~4.5 juveniles m–2 and a linear mixed model confirmed that home-range sizes in high-density areas (>4.5 juveniles m–2) were significantly smaller (34%) than those in low-density areas (after accounting for a significant effect of fish movement on our home-range estimates). Our results suggest that conspecific density may have negative and non-linear effects on home-range size, which could shape the spatial distribution of juveniles within a population, as well as influence individual fitness across local density gradients.

Dyslipidemia and Diabetic Macular Edema: A Systematic Review and Meta-Analysis

Topic: A systematic review and meta-analysis of dyslipidemia and diabetic macular edema (DME). 

Clinical Relevance: Diabetic macular edema causes impairment of vision in patients with diabetes, and dyslipidemia has been reported as a risk factor for its development. A systematic review with a meta-analysis was undertaken to examine the evidence of an association between dyslipidemia and DME. 

Methods: We defined eligibility criteria as randomized controlled trials (RCTs) and cohort, case-control, and cross-sectional studies reporting on the relationship between blood lipid levels and DME. We performed a literature search in MEDLINE, PubMed, and Embase from inception to September 2014. We used the NewcastleeOttawa scale to assess the quality of case-control, cross-sectional, and cohort studies, and the Cochrane risk of bias tool for RCTs. 

Results: The search strategy identified 4959 publications. After screening, we selected 21 articles for review (5 cross-sectional, 5 cohort, 7 case-control, and 4 RCTs). Meta-analysis of case-control studies revealed that mean levels of total serum cholesterol (TC), low-density lipoproteins (LDLs), and serum triglycerides (TGs) were significantly higher in patients with DME compared with those without DME (TC: 30.08; 95% confidence interval [CI], 21.14e39.02; P < 0.001; LDL: 18.62; 95% CI, 5.80e31.43; P < 0.05; TG: 24.82; 95% CI, 9.21e40.42; P < 0.05). Meta-analysis of RCTs did not show significant risk in worsening of hard exudates and severity of DME in the lipid-lowering group compared with placebo (hard exudates: relative risk, 1.00; 95% CI, 0.47e2.11; P ¼ 1.00; DME: relative risk, 1.18; 95% CI, 0.75e1.86; P ¼ 0.48). 

Conclusions: Despite evidence from the cohort studies and meta-analysis of the case-control studies suggesting a strong relationship between lipid levels and DME, this was not confirmed by the meta-analysis that included only prospective RCTs. Therefore, given the significant public health relevance of the topic, the relationship between lipid levels and DME deserves further investigation.

Helium line intensity ratio in microwave-generated plasmas

The line intensity ratio method provides a nonintrusive diagnostic for the measurement of electron temperature in microwave-generated plasmas. For optically thin plasmas of low density, a line intensity method using He I lines can often be used, and is based on the fact that the electron impact excitation rate coefficients for helium singlet and triplet states are insensitive to electron density but differ as a function of the electron temperature. Line intensity measurements are presented from microwave-generated helium plasmas. Both steady-state corona and collision-radiative theoretical models are used to evaluate the ground and excited state populations. The line ratio versus electron temperature obtained from both of these methods are compared with the results from measurements. However, it is not possible to diagnose the electron temperature from the line ratios alone due to the presence of significant opacity and nonnegligible 1s2s S-3 metastable fraction in the plasma. (C) 2004 American Institute of Physics.