Intelligent Management of Inter-Thread Synchronization Dependencies for Concurrent Programs.

Power dissipation limits and design complexity have made the microprocessor industry less successful in improving the performance of monolithic processors, even though semiconductor technology continues to scale. Consequently, chip multiprocessors (CMPs) have become a standard for all ranges of computing from cellular phones to high-performance servers. As sufficient thread level parallelism (TLP) is necessary to exploit the computational power provided by CMPs, most performance-aware programmers need to parallelize their programs. For shared memory multi-threaded programs, synchronization mechanisms such as mutexes, barriers, and condition variables, are used to enforce the threads to interact with each other in the way the programmers intended. However, employing synchronization operations in both correct and efficient way at the same time is extremely difficult, and there have been trade-offs between programmability and efficiency of using synchronizations. This thesis proposes a collection of works that increase the programmability and efficiency of concurrent programs by intelligently managing the synchronization operations. First, we focus on mutex locks and unlocks. Many concurrency bug detection tools and automated bug fixers rely on the precise identification of critical sections guarded by lock/unlock operations. We suggest a practical lock/unlock pairing mechanism that combines static analysis with dynamic instrumentation to identify critical sections in POSIX multi-threaded C/C++ programs. Second, we present Dynamic Core Boosting (DCB) to accelerate critical paths in multi-thread programs. Inter-thread dependencies through synchronizations form critical paths. These critical paths are major performance bottlenecks for concurrent programs, and they are exacerbated by workload imbalances in performance asymmetric CMPs. DCB coordinates its compiler, runtime subsystem, and architecture to mitigates such performance bottlenecks. Finally, we propose exploiting synchronization operations for better energy efficiency through dynamic power management.PhDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/108886/1/netforce_1.pd

Studying Clouds and Aerosols with Lidar Depolarization Ratio and Backscatter Relationships

This dissertation consists of three parts, each devoted to a particular issue of significant importance for CALIPSO lidar observation of depolarization ratio (delta) and backscatter (gamma?) to improve current understanding of the microphysical properties of clouds and aerosols. The relationships between depolarization ratio and backscatter allow us to retrieve particle thermodynamic phase and shape and/or orientation of aerosols and clouds. The first part is devoted to the investigation of the relationships between lidar backscatter and the corresponding depolarization ratio for different cloud classifications and aerosol types. For each cloud and aerosol types, layer-averaged backscatter and backscattering depolarization ratio from the CALIPSO measurements are discussed. The present results demonstrate the unique capabilities of the CALIPSO lidar instrument for determining cloud phase and aerosols subtypes. In the second part, we evaluate the MODIS IR cloud phase with the CALIPSO cloud products. The three possible misclassifications of MODIS IR cloud phasealgorithm, which are studied by Nasiri and Kahn (2008) with radiative transfer modeling, are tested by comparing between MODIS IR phase and CALIOP observations. The current results support their hypotheses, which is that the MODIS phase algorithm may tend to classify thin cirrus clouds as water clouds or mixed phase clouds or unknown, and classify midlevel and/or mid-temperature clouds as mixed or unknown phase. In the third part, we present a comparison of mineral dust aerosol retrievals from two instruments, MODIS and CALIPSO lidar. And, we implement and evaluate a new mineral dust detection algorithm based on the analysis of thin dust radiative signature. In comparison, three commonly used visible and IR mineral dust detection algorithms, including BTD procedure, D parameter method, and multi-channel image algorithm, are evaluated with CALIPSO aerosol classification. The comparison reveals that those dust detection algorithms are not effective for optically thin dust layers, but for thick dust storm. The new algorithm using discriminant analysis with CALIPSO observation is much better in detecting thin dust layer of optical thickness between 0.1 and 2

Spectral Dependence of MODIS Cloud Droplet Effective Radius Retrievals for Marine Boundary Layer Clouds

Low-level warm marine boundary layer (MBL) clouds cover large regions of Earth's surface. They have a significant role in Earth's radiative energy balance and hydrological cycle. Despite the fundamental role of low-level warm water clouds in climate, our understanding of these clouds is still limited. In particular, connections between their properties (e.g. cloud fraction, cloud water path, and cloud droplet size) and environmental factors such as aerosol loading and meteorological conditions continue to be uncertain or unknown. Modeling these clouds in climate models remains a challenging problem. As a result, the influence of aerosols on these clouds in the past and future, and the potential impacts of these clouds on global warming remain open questions leading to substantial uncertainty in climate projections. To improve our understanding of these clouds, we need continuous observations of cloud properties on both a global scale and over a long enough timescale for climate studies. At present, satellite-based remote sensing is the only means of providing such observations

Actin Cytoskeleton and Golgi Involvement in Barley stripe mosaic virus Movement and Cell Wall Localization of Triple Gene Block Proteins.

Barley stripe mosaic virus (BSMV) induces massive actin filament thickening at the infection front of infected Nicotiana benthamiana leaves. To determine the mechanisms leading to actin remodeling, fluorescent protein fusions of the BSMV triple gene block (TGB) proteins were coexpressed in cells with the actin marker DsRed: Talin. TGB ectopic expression experiments revealed that TGB3 is a major elicitor of filament thickening, that TGB2 resulted in formation of intermediate DsRed:Talin filaments, and that TGB1 alone had no obvious effects on actin filament structure. Latrunculin B (LatB) treatments retarded BSMV cell-to-cell movement, disrupted actin filament organization, and dramatically decreased the proportion of paired TGB3 foci appearing at the cell wall (CW). BSMV infection of transgenic plants tagged with GFP-KDEL exhibited membrane proliferation and vesicle formation that were especially evident around the nucleus. Similar membrane proliferation occurred in plants expressing TGB2 and/or TGB3, and DsRed: Talin fluorescence in these plants colocalized with the ER vesicles. TGB3 also associated with the Golgi apparatus and overlapped with cortical vesicles appearing at the cell periphery. Brefeldin A treatments disrupted Golgi and also altered vesicles at the CW, but failed to interfere with TGB CW localization. Our results indicate that actin cytoskeleton interactions are important in BSMV cell-to-cell movement and for CW localization of TGB3

Characterization of Developmental- and Stress-Mediated Expression of Cinnamoyl-CoA Reductase in Kenaf ( Hibiscus cannabinus

Cinnamoyl-CoA reductase (CCR) is an important enzyme for lignin biosynthesis as it catalyzes the first specific committed step in monolignol biosynthesis. We have cloned a full length coding sequence of CCR from kenaf (Hibiscus cannabinus L.), which contains a 1,020-bp open reading frame (ORF), encoding 339 amino acids of 37.37 kDa, with an isoelectric point (pI) of 6.27 (JX524276, HcCCR2). BLAST result found that it has high homology with other plant CCR orthologs. Multiple alignment with other plant CCR sequences showed that it contains two highly conserved motifs: NAD(P) binding domain (VTGAGGFIASWMVKLLLEKGY) at N-terminal and probable catalytic domain (NWYCYGK). According to phylogenetic analysis, it was closely related to CCR sequences of Gossypium hirsutum (ACQ59094) and Populus trichocarpa (CAC07424). HcCCR2 showed ubiquitous expression in various kenaf tissues and the highest expression was detected in mature flower. HcCCR2 was expressed differentially in response to various stresses, and the highest expression was observed by drought and NaCl treatments

Characterization of Developmental-and Stress-Mediated Expression of Cinnamoyl-CoA Reductase in Kenaf (Hibiscus cannabinus L.)

Cinnamoyl-CoA reductase (CCR) is an important enzyme for lignin biosynthesis as it catalyzes the first specific committed step in monolignol biosynthesis. We have cloned a full length coding sequence of CCR from kenaf (Hibiscus cannabinus L.), which contains a 1,020-bp open reading frame (ORF), encoding 339 amino acids of 37.37 kDa, with an isoelectric point (pI) of 6.27 (JX524276, HcCCR2). BLAST result found that it has high homology with other plant CCR orthologs. Multiple alignment with other plant CCR sequences showed that it contains two highly conserved motifs: NAD(P) binding domain (VTGAGGFIASWMVKLLLEKGY) at N-terminal and probable catalytic domain (NWYCYGK). According to phylogenetic analysis, it was closely related to CCR sequences of Gossypium hirsutum (ACQ59094) and Populus trichocarpa (CAC07424). HcCCR2 showed ubiquitous expression in various kenaf tissues and the highest expression was detected in mature flower. HcCCR2 was expressed differentially in response to various stresses, and the highest expression was observed by drought and NaCl treatments

Women with Fibromyalgia Have Lower Levels of Calcium, Magnesium, Iron and Manganese in Hair Mineral Analysis

Little is known about hair mineral status in fibromyalgia patients. This study evaluated the characteristics of hair minerals in female patients with fibromyalgia compared with a healthy reference group. Forty-four female patients diagnosed with fibromyalgia according to the American College of Rheumatology criteria were enrolled as the case group. Ageand body mass index-matched data were obtained from 122 control subjects enrolled during visit for a regular health check-up. Hair minerals were analyzed and compared between the two groups. The mean age was 43.7 yr. General characteristics were not different between the two groups. Fibromyalgia patients showed a significantly lower level of calcium (775 µg/g vs 1,093 µg/g), magnesium (52 µg/g vs 72 µg/g), iron (5.9 µg/g vs 7.1 µg/g), copper (28.3 µg/g vs 40.2 µg/g) and manganese (140 ng/g vs 190 ng/g). Calcium, magnesium, iron, and manganese were loaded in the same factor using factor analysis; the mean of this factor was significantly lower in fibromyalgia group in multivariate analysis with adjustment for potential confounders. In conclusion, the concentrations of calcium, magnesium, iron, and manganese in the hair of female patients with fibromyalgia are lower than of controls, even after adjustment of potential confounders

Ultrasonographic scoring system score versus liver stiffness measurement in prediction of cirrhosis

Background/AimsWe compared the cirrhosis-prediction accuracy of an ultrasonographic scoring system (USSS) combining six representative sonographic indices with that of liver stiffness measurement (LSM) by transient elastography, and prospectively investigated the correlation between the USSS score and LSM in predicting cirrhosis.MethodsTwo hundred and thirty patients with chronic liver diseases (187 men, 43 women; age, 50.4±9.5 y, mean±SD) were enrolled in this prospective study. The USSS produces a combined score for nodularity of the liver surface and edge, parenchyma echogenicity, presence of right-lobe atrophy, spleen size, splenic vein diameter, and abnormality of the hepatic vein waveform. The correlations of the USSS score and LSM with that of a pathological liver biopsy (METAVIR scoring system: F0-F4) were evaluated.ResultsThe mean USSS score and LSM were 7.2 and 38.0 kPa, respectively, in patients with histologically overt cirrhosis (F4, P=0.017) and 4.3 and 22.1 kPa in patients with fibrotic change without overt cirrhosis (F0-F3) (P=0.025). The areas under the receiver operating characteristic (ROC) curves of the USSS score and LSM for F4 patients were 0.849 and 0.729, respectively. On the basis of ROC curves, criteria of USSS ≥6: LSM ≥17.4 had a sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 89.2%:77.6%, 69.4%:61.4%, 86.5%:83.7%, 74.6%:51.9% and 0.83:0.73, respectively, in predicting F4.ConclusionsThe results indicate that this USSS has comparable efficacy to LSM in the diagnosis of cirrhosis

Effects of candesartan and propranolol combination therapy versus propranolol monotherapy in reducing portal hypertension

Background/AimsAngiotensin receptor blockers (ARBs) inhibit activated hepatic stellate cell contraction and are thought to reduce the dynamic portion of intrahepatic resistance. This study compared the effects of combined treatment using the ARB candesartan and propranolol versus propranolol monotherapy on portal pressure in patients with cirrhosis in a prospective, randomized controlled trial.MethodsBetween January 2008 and July 2009, 53 cirrhotic patients with clinically significant portal hypertension were randomized to receive either candesartan and propranolol combination therapy (26 patients) or propranolol monotherapy (27 patients). Before and 3 months after the administration of the planned medication, the hepatic venous pressure gradient (HVPG) was assessed in both groups. The dose of propranolol was subsequently increased from 20 mg bid until the target heart rate was reached, and the candesartan dose was fixed at 8 mg qd. The primary endpoint was the HVPG response rate; patients with an HVPG reduction of >20% of the baseline value or to <12 mmHg were defined as responders.ResultsThe mean portal pressure declined significantly in both groups, from 16 mmHg (range, 12-28 mmHg) to 13.5 mmHg (range, 6-20 mmHg) in the combination group (P<0.05), and from 17 mmHg (range, 12-27 mmHg) to 14 mmHg (range, 7-25 mmHg) in the propranolol monotherapy group (P<0.05). However, the medication-induced pressure reduction did not differ significantly between the two groups [3.5 mmHg (range, -3-11 mmHg) vs. 3 mmHg (range, -8-10 mmHg), P=0.674]. The response rate (55.6% vs. 61.5%, P=0.435) and the reductions in mean blood pressure or heart rate also did not differ significantly between the combination and monotherapy groups.ConclusionsThe addition of candesartan (an ARB) to propranolol confers no benefit relative to classical propranolol monotherapy for the treatment of portal hypertension, and is thus not recommended

The usefulness of non-invasive liver stiffness measurements in predicting clinically significant portal hypertension in cirrhotic patients: Korean data

Background/AimsLiver stiffness measurement (LSM) has been proposed as a non-invasive method for estimating the severity of fibrosis and the complications of cirrhosis. Measurement of the hepatic venous pressure gradient (HVPG) is the gold standard for assessing the presence of portal hypertension, but its invasiveness limits its clinical application. In this study we evaluated the relationship between LSM and HVPG, and the predictive value of LSM for clinically significant portal hypertension (CSPH) and severe portal hypertension in cirrhosis.MethodsLSM was performed with transient elastography in 59 consecutive cirrhotic patients who underwent hemodynamic HVPG investigations. CSPH and severe portal hypertension were defined as HVPG ≥10 and ≥12 mmHg, respectively. Linear regression analysis was performed to evaluate the relationship between LSM and HVPG. Diagnostic values were analyzed based on receiver operating characteristic (ROC) curves.ResultsA strong positive correlation between LSM and HVPG was observed in the overall population (r2=0.496, P<0.0001). The area under the ROC curve (AUROC) for the prediction of CSPH (HVPG ≥10 mmHg) was 0.851, and the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for an LSM cutoff value of 21.95 kPa were 82.5%, 73.7%, 86.8%, and 66.7%, respectively. The AUROC at prediction of severe portal hypertension (HVPG ≥12 mmHg) was 0.877, and the sensitivity, specificity, PPV, and NPV at LSM cutoff value of 24.25 kPa were 82.9%, 70.8%, 80.6%, and 73.9%, respectively.ConclusionsLSM exhibited a significant correlation with HVPG in patients with cirrhosis. LSM could be a non-invasive method for predicting CSPH and severe portal hypertension in Korean patients with liver cirrhosis