Prediction-Based Power-Performance Adaptation of Multithreaded Scientific Codes

Computing has recently reached an inflection point with the introduction of multicore processors. On-chip thread-level parallelism is doubling approximately every other year. Concurrency lends itself naturally to allowing a program to trade performance for power savings by regulating the number of active cores; however, in several domains, users are unwilling to sacrifice performance to save power. We present a prediction model for identifying energy-efficient operating points of concurrency in well-tuned multithreaded scientific applications and a runtime system that uses live program analysis to optimize applications dynamically. We describe a dynamic phase-aware performance prediction model that combines multivariate regression techniques with runtime analysis of data collected from hardware event counters to locate optimal operating points of concurrency. Using our model, we develop a prediction-driven phase-aware runtime optimization scheme that throttles concurrency so that power consumption can be reduced and performance can be set at the knee of the scalability curve of each program phase. The use of prediction reduces the overhead of searching the optimization space while achieving near-optimal performance and power savings. A thorough evaluation of our approach shows a reduction in power consumption of 10.8 percent, simultaneous with an improvement in performance of 17.9 percent, resulting in energy savings of 26.7 percent.

Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells

The retinal vascular endothelium is essential for angiogenesis and is involved in maintaining barrier selectivity and vascular tone. The aim of this study was to identify and quantify microRNAs and other small regulatory non-coding RNAs (ncRNAs) which may regulate these crucial functions. Primary bovine retinal microvascular endothelial cells (RMECs) provide a well-characterized in vitro system for studying angiogenesis. RNA extracted from RMECs was used to prepare a small RNA library for deep sequencing (Illumina Genome Analyzer). A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). In many cases, the most frequent isomiR differed from the sequence reported in miRBase. In addition, five novel microRNAs, 13 novel bovine orthologs of known human microRNAs and multiple new members of the miR-2284/2285 family were detected. Several similar to 30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one-third of all mapped reads. Inhibition of miR-21 with an LNA inhibitor significantly reduced proliferation, migration, and tube-forming capacity of RMECs. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Knockdown of miR-21 suggests a role for this microRNA in regulation of angiogenesis in the retinal microvasculature. J. Cell. Biochem. 113: 20982111, 2012. (C) 2012 Wiley Periodicals, Inc.

Voltage-activated currents in cardiac myocytes of the blue mussel, Mytilus edulis

Voltage-sensitive ionic currents were identified and characterised in ventricular myocytes of the bivalve mollusc, Mytilus edulis, using the whole-cell patch-clamp technique. Two outward currents could be distinguished. A potassium A current (I-A) activated at - 30 mV from a holding potential of - 60 mV. This transient current was inactivated by holding the cells at a potential of - 40 mV and was also blocked by applying 4-aminopyridine (3 mM) to the external bath solution. A second current was identified as a delayed rectifier (I-K). This also activated at - 30 mV but exhibited a sustained time course and was still activated at a holding potential of - 40 mV. Both outward currents were reduced in the presence of tetraethylammonium ions (30 mM). A small number of heart cells also showed an inward sodium current (I-Na). This current appeared at potentials more positive than - 50 mV, reached a maximum at - 20 mV, and decreased with further depolarisation. I-Na was inactivated at a holding potential of - 40 mV and was blocked by tetrodotoxin (1 mu M). A second inward current had a sustained time course and was not inactivated by holding the cell at a potential of -40 mV, and was also not abolished by tetrodotoxin. This current peaked at 0 mV, decreasing with further depolarisation. Furthermore, it was enhanced by the addition of barium ions (3 mM) to the bath and was blocked by external cobalt (2 mM) or nifedipine (15 mu M) These findings are consistent with this being an L-type calcium current (I-Ca) The possible physiological roles of these currents in M. edulis heart are discussed. (C) 1999 Elsevier Science Inc. All rights reserved.

Simultaneous, long-term monitoring of valve and cardiac activity in the blue mussel Mytilus edulis exposed to copper

Valve and cardiac activity were simultaneously measured in the blue mussel (Mytilus edulis) in response to 10 d copper exposure. Valve movements, heart rates and heart-rate variability were obtained non-invasively using a Musselmonitor(R) (valve activity) and a modified version of the Computer-Aided Physiological Monitoring system (CAPMON; cardiac activity). After 2 d exposure of mussels (4 individuals per treatment group) to a range of dissolved copper concentrations (0 to 12.5 mu M as CuCl2) median valve positions (% open) and median heart rates (beats per minute) declined as a function of copper concentration. Heart-rate variability (coefficient of variation for interpulse durations) rose in a concentration-dependent manner. The 48 h EC50 values (concentrations of copper causing 50% change) for valve positions, heart rates and heart-rate variability were 2.1, 0.8, and 0.06 mu M, respectively. Valve activity was weakly correlated with both heart rate (r = 0.48 +/- 0.02) and heart-rate variability (r = 0.32 +/- 0.06) for control individuals (0 mu M Cu2+). This resulted from a number of short enclosure events that did not coincide with a change in cardiac activity. Exposure of mussels to increasing copper concentrations (greater than or equal to 0.8 mu M) progressively reduced the correlation between valve activity and heart rates (r = 0 for individuals dosed with greater than or equal to 6.3 mu M Cu2+), while correlations between valve activity and heart-rate variability were unaffected. The poor correlations resulted from periods of valve flapping that were not mimicked by similar fluctuations in heart rate or heart-rate variability. The data suggest that the copper-induced bradycardia observed in mussels is not a consequence of prolonged valve closure.

The initial mode of action of copper on the cardiac physiology of the blue mussel, Mytilus edulis

Previous studies have shown that low levels of copper (down to 0.8 muM) induce bradycardia in the blue mussel (Mytilus edulis) and that this is not caused by prolonged Valve closure. The aim of this study was to determine the precise mechanism responsible. To establish if copper was directly affecting heart cell physiology, recordings of contractions from isolated ventricular strips were made using an isometric force transducer, in response to copper concentrations (as CuCl2) ranging between 1 muM and 1 mM. Inhibition of mechanical activity only occurred at 1 mM copper, suggesting that the copper-induced bradycardia observed in whole animals cannot be attributed to direct cardiotoxicity. Effects of copper on the cardiac nerves were subsequently examined. Following removal of visceral ganglia (from where the cardiac nerves originate), exposure to 12.5 muM copper had no effect on the heart rate of whole animals. The effect of copper on the heart rate of mussels could not be abolished by depletion of the monoamine content of the animal using reserpine. However, pre-treatment of the animals with alpha -bungarotoxin considerably reduced the sensitivity of the heart to copper. These results indicated that the influence of copper on the heart of M. edulis might be mediated by a change in the activity of cholinergic nerves to heart. In the final experiments, mussels were injected with either benzoquinonium or D-tubocurarine, prior to copper exposure, in an attempt to selectively block the inhibitory or excitatory cholinoreceptors of the heart. Only benzoquinonium decreased the susceptibility of the heart to copper, suggesting that copper affects the cardiac activity of blue mussels by stimulating inhibitory cholinergic nerves to the heart. (C) 2001 Elsevier Science B.V. All rights reserved.

Effects of the organophosphorous pesticide, dimethoate, on cardiac and acetylcholinesterase (AChE) activity in the shore crab Carcinus maenas

The potential use of biochemical and physiological responses as biomarkers of organophosphate exposure and/or effect were assessed in the shore crab (Carcinus maenas). Male crabs were assigned to one of four dimethoate treatments (0, 0.5, 1.0 or 2.0 mg 1(-1)). Cardiac activity was measured non-invasively before and during dimethoate exposure using automated interpulse duration assessment. Heart rates decreased significantly in a concentration-dependent manner (p

Automated interpulse-duration assessment (AIDA): A new technique for detecting disturbances in cardiac activity in selected macroinvertebrates

An Automated Interpulse Duration Assessment system (AIDA) is described which permits detection of irregularities in cardiac rhythms in selected invertebrates. The sensitivity of AIDA was demonstrated by its ability to detect handling stress in mussels (Mytilus edulis) that was not evident when measuring heart rate alone. Changes in cardiac activity patterns of crabs (Carcinus maenas) held in the laboratory for up to 10 wk was also examined using the new technique. The frequency distribution of interpulse duration changed significantly as the nutritional state changed. Potential applications of the AIDA system are discussed.

Feedback via Ca²⁺-activated ion channels modulates endothelin 1 signaling in retinal arteriolar smooth muscle

PURPOSE: To investigate the role of feedback by Ca²?-sensitive plasma-membrane ion channels in endothelin 1 (Et1) signaling in vitro and in vivo. Methods. Et1 responses were imaged from Fluo-4-loaded smooth muscle in isolated segments of rat retinal arteriole using two-dimensional (2-D) confocal laser microscopy. Vasoconstrictor responses to intravitreal injections of Et1 were recorded in the absence and presence of appropriate ion channel blockers using fluorescein angiograms imaged using a confocal scanning laser ophthalmoscope. Results. Et1 (10 nM) increased both basal [Ca²?](i) and the amplitude and frequency of Ca²?-waves in retinal arterioles. The Ca²?-activated Cl?-channel blockers DIDS and 9-anthracene carboxylic acid (9AC) blocked Et1-induced increases in wave frequency, and 9AC also inhibited the increase in amplitude. Iberiotoxin, an inhibitor of large conductance (BK) Ca²?-activated K?-channels, increased wave amplitude in the presence of Et1 but had no effect on frequency. None of these drugs affected basal [Ca²?](i). The voltage-operated Ca²?-channel inhibitor nimodipine inhibited wave frequency and amplitude and also lowered basal [Ca²?](i) in the presence of Et1. Intravitreal injection of Et1 caused retinal arteriolar vasoconstriction. This was inhibited by DIDS but not by iberiotoxin or penitrem A, another BK-channel inhibitor. Conclusions. Et1 evokes increases in the frequency of arteriolar Ca²?-waves in vitro, resulting in vasoconstriction in vivo. These responses, initiated by release of stored Ca²?, also require positive feedback via Ca²?-activated Cl?-channels and L-type Ca²?-channels.

Fast Retinal Vessel Detection and Measurement Using Wavelets and Edge Location Refinement

The relationship between changes in retinal vessel morphology and the onset and progression of diseases such as diabetes, hypertension and retinopathy of prematurity (ROP) has been the subject of several large scale clinical studies. However, the difficulty of quantifying changes in retinal vessels in a sufficiently fast, accurate and repeatable manner has restricted the application of the insights gleaned from these studies to clinical practice. This paper presents a novel algorithm for the efficient detection and measurement of retinal vessels, which is general enough that it can be applied to both low and high resolution fundus photographs and fluorescein angiograms upon the adjustment of only a few intuitive parameters. Firstly, we describe the simple vessel segmentation strategy, formulated in the language of wavelets, that is used for fast vessel detection. When validated using a publicly available database of retinal images, this segmentation achieves a true positive rate of 70.27%, false positive rate of 2.83%, and accuracy score of 0.9371. Vessel edges are then more precisely localised using image profiles computed perpendicularly across a spline fit of each detected vessel centreline, so that both local and global changes in vessel diameter can be readily quantified. Using a second image database, we show that the diameters output by our algorithm display good agreement with the manual measurements made by three independent observers. We conclude that the improved speed and generality offered by our algorithm are achieved without sacrificing accuracy. The algorithm is implemented in MATLAB along with a graphical user interface, and we have made the source code freely available. 

Pharmacological profiling of store-operated Ca(2+) entry in retinal arteriolar smooth muscle

Objective: Pharmacological profiling of store-operated Ca(2+) entry (SOCE) and molecular profiling of ORAI and TRPC expression in arterioles. 
Methods: Fura-2 based microfluorimetry was used to assess CPA-induced SOCE in rat retinal arteriolar myocytes. Arteriolar ORAI and TRP transcript expression were screened using RT-PCR. 
Results: SKF96365 and LOE908 blocked SOCE (IC(50) s of 1.2µM and 1.4µM, respectively). Gd(3+) and La(3+) potently inhibited SOCE (IC(50) s of 21nM and 42nM, respectively), but Ni(2+) showed lower potency (IC(50) = 11.6µM). 2-aminoethyldiphenyl borate (2APB) inhibited SOCE (IC(50) = 3.7µM) but enhanced basal influx (>100µM). Verapamil and nifedipine had no effect at concentrations that inhibit L-type Ca(2+) channels, but diltiazem inhibited SOCE by approximately 40% (=0.1µM). RT-PCR demonstrated transcript expression for ORAI 1, 2 and 3, and TRPC1, 3, 4 and 7. Transcripts for TRPV1 and 2, which are activated by 2APB, were also expressed. 
Conclusion: The pharmacological profile of SOCE in retinal arteriolar smooth muscle appears unique when compared to other vascular tissues. This suggests that the molecular mechanisms underlying SOCE can differ, even in closely related tissues. Taken together, the pharmacological and molecular data are most consistent with involvement of TRPC1 in SOCE, although involvement of ORAI or other TRPC channels cannot be excluded. © 2012 John Wiley & Sons Ltd.