A profile-based tool for finding pipeline parallelism in sequential programs

Traditional static analysis fails to auto-parallelize programs with a complex control and data flow. Furthermore, thread-level parallelism in such programs is often restricted to pipeline parallelism, which can be hard to discover by a programmer. In this paper we propose a tool that, based on profiling information, helps the programmer to discover parallelism. The programmer hand-picks the code transformations from among the proposed candidates which are then applied by automatic code transformation techniques.

This paper contributes to the literature by presenting a profiling tool for discovering thread-level parallelism. We track dependencies at the whole-data structure level rather than at the element level or byte level in order to limit the profiling overhead. We perform a thorough analysis of the needs and costs of this technique. Furthermore, we present and validate the belief that programs with complex control and data flow contain significant amounts of exploitable coarse-grain pipeline parallelism in the program’s outer loops. This observation validates our approach to whole-data structure dependencies. As state-of-the-art compilers focus on loops iterating over data structure members, this observation also explains why our approach finds coarse-grain pipeline parallelism in cases that have remained out of reach for state-of-the-art compilers. In cases where traditional compilation techniques do find parallelism, our approach allows to discover higher degrees of parallelism, allowing a 40% speedup over traditional compilation techniques. Moreover, we demonstrate real speedups on multiple hardware platforms.

Antimicrobic susceptibility and plasmid profile analysis as identity tests for multiple blood isolates of coagulase-negative staphylococci

We compared a disk diffusion antimicrobic susceptibility panel with plasmid DNA profiles as tests for identity of 106 isolates of coagulase-negative staphylococci cultured from the blood of 45 patients on multiple occasions. The antimicrobic panel included penicillin, oxacillin, clindamycin, trimethoprim-sulfamethoxazole, chloramphenicol, tetracycline, tobramycin, kanamycin, and gentamicin. Nineteen patterns of antimicrobic susceptibility were found. The most common pattern was present in 25% of the isolates, and at least one isolate from 31% of the patients had this pattern. Forty-seven distinct plasmid DNA profiles were found. The most common plasmid profile was present in 8.5% of the isolates, and at least one isolate from 15% of the patients had this profile. Twenty-eight patients had multiple isolates that were identical by plasmid profile analysis. Twenty-seven (96%) of these patients had isolates that were also identical by antimicrobic susceptibility. Nineteen patients had multiple isolates that were different by plasmid profile analysis. In 18 (95%) of these patients, the isolates were also different by antimicrobic susceptibility. Although plasmid DNA profile analysis is a more discriminating tool, these data confirm that a selected disk diffusion antimicrobic susceptibility panel may be used to screen multiple blood isolates of coagulase-negative staphylococci for identity or differences.

Docosahexaenoic acid induces an anti-inflammatory profile in lipopolysaccharide-stimulated human THP-1 macrophages more effectively than eicosapentaenoic acid

A number of studies have investigated the effects of fish oil on the production of pro-inflammatory cytokines using peripheral blood mononuclear cell models. The majority of these studies have employed heterogeneous blends of long-chain n-3 polyunsaturated fatty acids (PUFA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which preclude examination of the individual effects of LC n-3 PUFA. This study investigated the differential effects of pure EPA and DHA on cytokine expression and nuclear factor kappaB (NF-kappaB) activation in human THP-1 monocyte-derived macrophages. Pretreatment with 100 microM EPA and DHA significantly decreased lipopolysaccharide (LPS)-stimulated THP-1 macrophage tumor necrosis factor (TNF) alpha, interleukin (IL) 1beta and IL-6 production (P

Distinctive Profile of IsomiR Expression and Novel MicroRNAs in Rat Heart Left Ventricle

MicroRNAs (miRNAs) are single-stranded non-coding RNAs that negatively regulate target gene expression through mRNA cleavage or translational repression. There is mounting evidence that they play critical roles in heart disease. The expression of known miRNAs in the heart has been studied at length by microarray and quantitative PCR but it is becoming evident that microRNA isoforms (isomiRs) are potentially physiologically important. It is well known that left ventricular (patho)physiology is influenced by transmural heterogeneity of cardiomyocyte phenotype, and this likely reflects underlying heterogeneity of gene expression. Given the significant role of miRNAs in regulating gene expression, knowledge of how the miRNA profile varies across the ventricular wall will be crucial to better understand the mechanisms governing transmural physiological heterogeneity. To determinine miRNA/isomiR expression profiles in the rat heart we investigated tissue from different locations across the left ventricular wall using deep sequencing. We detected significant quantities of 145 known rat miRNAs and 68 potential novel orthologs of known miRNAs, in mature, mature* and isomiR formation. Many isomiRs were detected at a higher frequency than their canonical sequence in miRBase and have different predicted targets. The most common miR-133a isomiR was more effective at targeting a construct containing a sequence from the gelsolin gene than was canonical miR-133a, as determined by dual-fluorescence assay. We identified a novel rat miR-1 homolog from a second miR-1 gene; and a novel rat miRNA similar to miR-676. We also cloned and sequenced the rat miR-486 gene which is not in miRBase (v18). Signalling pathways predicted to be targeted by the most highly detected miRNAs include Ubiquitin-mediated Proteolysis, Mitogen-Activated Protein Kinase, Regulation of Actin Cytoskeleton, Wnt signalling, Calcium Signalling, Gap junctions and Arrhythmogenic Right Ventricular Cardiomyopathy. Most miRNAs are not expressed in a gradient across the ventricular wall, with exceptions including miR-10b, miR-21, miR-99b and miR-486.

Freeze-dried strawberry powder improves lipid profile and lipid peroxidation in women with metabolic syndrome:baseline and post intervention effects

Strawberry flavonoids are potent antioxidants and anti-inflammatory agents that have been shown to reduce cardiovascular disease risk factors in prospective cohort studies. Effects of strawberry supplementation on metabolic risk factors have not been studied in obese populations. We tested the hypothesis that freeze-dried strawberry powder (FSP) will lower fasting lipids and biomarkers of oxidative stress and inflammation at four weeks compared to baseline. We also tested the tolerability and safety of FSP in subjects with metabolic syndrome. FSP is a concentrated source of polyphenolic flavonoids, fiber and phytosterols.

Nuclear magnetic resonance-determined lipoprotein subclass profile in the DCCT/EDIC cohort:associations with carotid intima-media thickness

To relate nuclear magnetic resonance lipoprotein subclass profiles (NMR-LSP) and other lipoprotein-related factors with carotid intima-media thickness (IMT) in Type 1 diabetes.

Killer immunoglobulin-like Receptors (KIR) haplogroups A and B track with Natural Killer Cells and Cytokine Profile in Aged Subjects: Observations from Octo/Nonagenarians in the Belfast Elderly Longitudinal Free-living Aging STudy (BELFAST)

Background: Natural Killer Cells (NK) play an important role in detection and elimination of virus-infected, damaged or cancer cells. NK cell function is guided by expression of Killer Immunoglobulin-like Receptors (KIRs) and contributed to by the cytokine milieu. KIR molecules are grouped on NK cells into stimulatory and inhibitory KIR haplotypes A and B, through which NKs sense and tolerate HLA self-antigens or up-regulate the NK-cytotoxic response to cells with altered HLA self-antigens, damaged by viruses or tumours. We have previously described increased numbers of NK and NK-related subsets in association with sIL-2R cytokine serum levels in BELFAST octo/nonagenarians. We hypothesised that changes in KIR A and B haplotype gene frequencies could explain the increased cytokine profiles and NK compartments previously described in Belfast Elderly Longitudinal Free-living Aging STudy (BELFAST) octo/nonagenarians, who show evidence of ageing well.

Results: In the BELFAST study, 24% of octo/nonagenarians carried the KIR A haplotype and 76% KIR B haplotype with no differences for KIR A haplogroup frequency between male or female subjects (23% v 24%; p=0.88) or for KIR B haplogroup (77% v 76%; p=0.99). Octo/nonagenarian KIR A haplotype carriers showed increased NK numbers and percentage compared to Group B KIR subjects (p=0.003; p=0.016 respectively). There were no KIR A/ B haplogroup-associated changes for related CD57+CD8 (high or low) subsets. Using logistic regression, KIR B carriers were predicted to have higher IL-12 cytokine levels compared to KIR A carriers by about 3% (OR 1.03, confidence limits CI 0.99–1.09; p=0.027) and 14% higher levels for TGF-ß (active), a cytokine with an anti-inflammatory role, (OR 1.14, confidence limits CI 0.99–1.09; p=0.002).

Conclusion: In this observational study, BELFAST octo/nonagenarians carrying KIR A haplotype showed higher NK cell numbers and percentage compared to KIR B carriers. Conversely, KIR B haplotype carriers, with genes encoding for activating KIRs, showed a tendency for higher serum pro-inflammatory cytokines compared to KIR A carriers. While the findings in this study should be considered exploratory they may serve to stimulate debate about the immune signatures of those who appear to age slowly and who represent a model for good quality survivor-hood.© 2013 Rea et al.; licensee BioMed Central Ltd.

The lateritic profile of Balkouin, Burkina Faso: geochemistry, mineralogy and genesis

This study reports on the geochemical and mineralogical characterization of a lateritic profile cropping out in the Balkouin area, Central Burkina Faso, aimed at obtaining a better understanding of the processes responsible for the formation of the laterite itself and the constraints to its development. The lateritic profile rests on a Paleoproterozoic basement mostly composed of granodioritic rocks related to the Eburnean magmatic cycle passing upwards to saprolite and consists of four main composite horizons (bottom to top): kaolinite and clay-rich horizons, mottled laterite and iron-rich duricrust. In order to achieve such a goal, a multi-disciplinary analytical approach was adopted, which includes inductively coupled plasma (ICP) atomic emission and mass spectrometries (ICP-AES and ICP-MS respectively), X-ray powder diffraction (XRPD), scanning electron microscopy with energy dispersive spectrometry (SEM-EDS) and micro-Raman spectroscopy.

The geochemical data, and particularly the immobile elements distribution and REE patterns, show that the Balkouin laterite is the product of an in situ lateritization process that involved a strong depletion of the more soluble elements (K, Mg, Ca, Na, Rb, Sr and Ba) and an enrichment in Fe; Si was also removed, particularly in the uppermost horizons. All along the profile the change in composition is coupled with important changes in mineralogy. In particular, the saprolite is characterized by occurrence of abundant albitic plagioclase, quartz and nontronite; kaolinite is apparently absent. The transition to the overlying lateritic profile marks the breakdown of plagioclase and nontronite, thus allowing kaolinite to become one of the major components upwards, together with goethite and quartz. The upper part of the profile is strongly enriched in hematite (+ kaolinite). Ti oxides (at least in part as anatase) and apatite are typical accessory phases, while free aluminum hydroxides are notably absent. Mass change calculations emphasize the extent of the mass loss, which exceeds 50 wt% (and often 70 wt%) for almost all horizons; only Fe was significantly concentrated in the residual system.

The geochemical and mineralogical features suggest that the lateritic profile is the product of a continuous process that gradually developed from the bedrock upwards, in agreement with the Schellmann classic genetic model. The laterite formation must have occurred at low pH (? 4.5) and high Eh (? 0.4) values, i.e., under acidic and oxidizing environments, which allowed strongly selective leaching conditions. The lack of gibbsite and bohemite is in agreement with the compositional data: the occurrence of quartz (± amorphous silica) all along the profile was an inhibiting factor for the formation of free aluminum hydroxides.