Towards Efficient Resource Provisioning in Hadoop

Considering recent exponential growth in the amount of information processed in Big Data, the high energy consumed by data processing engines in datacenters has become a major issue, underlining the need for efficient resource allocation for better energy-efficient computing. This thesis proposes the Best Trade-off Point (BToP) method which provides a general approach and techniques based on an algorithm with mathematical formulas to find the best trade-off point on an elbow curve of performance vs. resources for efficient resource provisioning in Hadoop MapReduce and Apache Spark. Our novel BToP method is expected to work for any applications and systems which rely on a tradeoff curve with an elbow shape, non-inverted or inverted, for making good decisions. This breakthrough method for optimal resource provisioning was not available before in the scientific, computing, and economic communities. To illustrate the effectiveness of the BToP method on the ubiquitous Hadoop MapReduce, our Terasort experiment shows that the number of task resources recommended by the BToP algorithm is always accurate and optimal when compared to the ones suggested by three popular rules of thumbs. We also test the BToP method on the emerging cluster computing framework Apache Spark running in YARN cluster mode. Despite the effectiveness of Spark’s robust and sophisticated built-in dynamic resource allocation mechanism, which is not available in MapReduce, the BToP method could still consistently outperform it according to our Spark-Bench Terasort test results. The performance efficiency gained from the BToP method not only leads to significant energy saving but also improves overall system throughput and prevents cluster underutilization in a multi-tenancy environment. In General, the BToP method is preferable for workloads with identical resource consumption signatures in production environment where job profiling for behavioral replication will lead to the most efficient resource provisioning

Towards efficient resource provisioning in MapReduce

The paper presents a novel approach and algorithm with mathematical formula for obtaining the exact optimal number of task resources for any workload running on HadoopMapReduce. In the era of Big Data, energy efficiency has become an important issue for the ubiquitous Hadoop MapReduce framework. However, the question of what is the optimal number of tasks required for a job to get the most efficient performance from MapReduce still has no definite answer. Our algorithm for optimal resource provisioning allows users to identify the best trade-off point between performance and energy efficiency on the runtime elbow curve fitted from sampled executions on the target cluster for subsequent behavioral replication. Our verification and comparison show that the currently well-known rules of thumb for calculating the required number of reduce tasks are inaccurate and could lead to significant waste of computing resources and energy with no further improvement in execution time

Snowmelt onset hinders bromine monoxide heterogeneous recycling in the Arctic

Reactive bromine radicals (bromine atoms, Br, and bromine monoxide, BrO) deplete ozone and alter tropospheric oxidation chemistry during the Arctic springtime (February–June). As spring transitions to summer (May–June) and snow begins to melt, reactive bromine events cease and BrO becomes low in summer. In this study, we explore the relationship between the end of the reactive bromine season and snowmelt timing. BrO was measured by Multi‐AXis Differential Optical Absorption Spectrometer at Utqiaġvik (Barrow), AK, from 2012 to 2016 and on drifting buoys deployed in Arctic sea ice from 2011 to 2016, a total of 13 site and year combinations. The BrO seasonal end date (SED) was objectively determined and was compared to surface‐air‐temperature‐derived melt onset date (MOD). The SED was highly correlated with the MOD (N = 13, R2 = 0.983, RMS = 1.9 days), and BrO is only observed at subfreezing temperatures. In subsets of these sites and years where ancillary data were available, we observed that snowpack depth reduced and rain precipitation occurred within a few days of the SED. These data are consistent with snowpack melting hindering BrO recycling, which is necessary to maintain enhanced BrO concentrations. With a projected warmer Arctic, a shift to earlier snowmelt seasons could alter the timing and role of halogen chemical reactions in the Arctic with impacts on ozone depletion and mercury deposition.Plain Language SummaryReactive bromine events in the Arctic are common in spring and deplete ozone and cause mercury deposition. These events are affected by snow and ice, which are changing in the Arctic; therefore, we need to understand how environmental conditions affect reactive bromine chemistry. We find that the reactive bromine season ends when snowpack begins to melt. Through these full seasonal observations, we find that reactive bromine events occur to warmer temperatures than previously reported, with 0°C being the observed threshold above which reactive bromine is absent. We also find that snow appears necessary for reactive bromine chemistry and rain stops this chemistry. Earlier snowmelt in a warmer Arctic would end the reactive bromine season earlier, decreasing late springtime ozone depletion and mercury deposition.Key PointsSnowmelt onset hinders reactive bromine heterogeneous recycling and ends season of reactive bromine eventsReactive bromine events occur at subfreezing air temperatures but not at higher temperaturesSnow appears necessary for reactive bromine heterogeneous recycling, and rainwater can terminate this chemistryPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138295/1/jgrd53947_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138295/2/jgrd53947.pd

Modelling the health impact of food taxes and subsidies with price elasticities: the case for additional scaling of food consumption using the total food expenditure elasticity

Background Food taxes and subsidies are one intervention to address poor diets. Price elasticity (PE) matrices are commonly used to model the change in food purchasing. Usually a PE matrix is generated in one setting then applied to another setting with differing starting consumption and prices of foods. This violates econometric assumptions resulting in likely misestimation of total food consumption. We illustrate rescaling all consumption after applying a PE matrix using a total food expenditure elasticity (TFEe, the expenditure elasticity for all food combined given the policy induced change in the total price of food). We use case studies of NZ$2 per 100g saturated fat (SAFA) tax, NZ$0.4 per 100g sugar tax, and a 20% fruit and vegetable (F&V) subsidy. Methods We estimated changes in food purchasing using a NZ PE matrix applied conventionally, then with TFEe adjustment. Impacts were quantified for total food expenditure and health adjusted life years (HALYs) for the total NZ population alive in 2011 over the rest of their lifetime using a multistate lifetable model. Results Two NZ studies gave TFEes of 0.68 and 0.83, with international estimates ranging from 0.46 to 0.90. Without TFEe adjustment, total food expenditure decreased with the tax policies and increased with the F&V subsidy, implausible directions of shift given economic theory. After TFEe adjustment, HALY gains reduced by a third to a half for the two taxes and reversed from an apparent health loss to a health gain for the F&V subsidy. With TFEe adjustment, HALY gains (in 1000s) were 1,805 (95% uncertainty interval 1,337 to 2,340) for the SAFA tax, 1,671 (1,220 to 2,269) for the sugar tax, and 953 (453 to 1,308) for the F&V subsidy. Conclusions If PE matrices are applied in settings beyond where they were derived, additional scaling is likely required. We suggest that the TFEe is a useful scalar

Platelet-activating factor is crucial in psoralen and ultraviolet A-induced immune suppression, inflammation, and apoptosis.

Psoralen plus UVA (PUVA) is used as a very effective treatment modality for various diseases, including psoriasis and cutaneous T-cell lymphoma. PUVA-induced immune suppression and/or apoptosis are thought to be responsible for the therapeutic action. However, the molecular mechanisms by which PUVA acts are not well understood. We have previously identified platelet-activating factor (PAF), a potent phospholipid mediator, as a crucial substance triggering ultraviolet B radiation-induced immune suppression. In this study, we used PAF receptor knockout mice, a selective PAF receptor antagonist, a COX-2 inhibitor (presumably blocking downstream effects of PAF), and PAF-like molecules to test the role of PAF receptor binding in PUVA treatment. We found that activation of the PAF pathway is crucial for PUVA-induced immune suppression (as measured by suppression of delayed type hypersensitivity to Candida albicans) and that it plays a role in skin inflammation and apoptosis. Downstream of PAF, interleukin-10 was involved in PUVA-induced immune suppression but not inflammation. Better understanding of PUVA\u27s mechanisms may offer the opportunity to dissect the therapeutic from the detrimental (ie, carcinogenic) effects and/or to develop new drugs (eg, using the PAF pathway) that act like PUVA but have fewer side effects

Sparing of the Dystrophin-Deficient Cranial Sartorius Muscle Is Associated with Classical and Novel Hypertrophy Pathways in GRMD Dogs

Both Duchenne and golden retriever muscular dystrophy (GRMD) are caused by dystrophin deficiency. The Duchenne muscular dystrophy sartorius muscle and orthologous GRMD cranial sartorius (CS) are relatively spared/hypertrophied. We completed hierarchical clustering studies to define molecular mechanisms contributing to this differential involvement and their role in the GRMD phenotype. GRMD dogs with larger CS muscles had more severe deficits, suggesting that selective hypertrophy could be detrimental. Serial biopsies from the hypertrophied CS and other atrophied muscles were studied in a subset of these dogs. Myostatin showed an age-dependent decrease and an inverse correlation with the degree of GRMD CS hypertrophy. Regulators of myostatin at the protein (AKT1) and miRNA (miR-539 and miR-208b targeting myostatin mRNA) levels were altered in GRMD CS, consistent with down-regulation of myostatin signaling, CS hypertrophy, and functional rescue of this muscle. mRNA and proteomic profiling was used to identify additional candidate genes associated with CS hypertrophy. The top-ranked network included α-dystroglycan and like-acetylglucosaminyltransferase. Proteomics demonstrated increases in myotrophin and spectrin that could promote hypertrophy and cytoskeletal stability, respectively. Our results suggest that multiple pathways, including decreased myostatin and up-regulated miRNAs, α-dystroglycan/like-acetylglucosaminyltransferase, spectrin, and myotrophin, contribute to hypertrophy and functional sparing of the CS. These data also underscore the muscle-specific responses to dystrophin deficiency and the potential deleterious effects of differential muscle involvement

Snowpack measurements suggest role for multi-year sea ice regions in Arctic atmospheric bromine and chlorine chemistry

As sources of reactive halogens, snowpacks in sea ice regions control the oxidative capacity of the Arctic atmosphere. However, measurements of snowpack halide concentrations remain sparse, particularly in the high Arctic, limiting our understanding of and ability to parameterize snowpack participation in tropospheric halogen chemistry. To address this gap, we measured concentrations of chloride, bromide, and sodium in snow samples collected during polar spring above remote multi-year sea ice (MYI) and first-year sea ice (FYI) north of Greenland and Alaska, as well as in the central Arctic, and compared these measurements to a larger dataset collected in the Alaskan coastal Arctic by Krnavek et al. (2012). Regardless of sea ice region, these surface snow samples generally featured lower salinities, compared to coastal snow. Surface snow in FYI regions was typically enriched in bromide and chloride compared to seawater, indicating snowpack deposition of bromine and chlorine-containing trace gases and an ability of the snowpack to participate further in bromine and chlorine activation processes. In contrast, surface snow in MYI regions was more often depleted in bromide, indicating it served as a source of bromine-containing trace gases to the atmosphere prior to sampling. Measurements at various snow depths indicate that the deposition of sea salt aerosols and halogen-containing trace gases to the snowpack surface played a larger role in determining surface snow halide concentrations compared to upward brine migration from sea ice. Calculated enrichment factors for bromide and chloride, relative to sodium, in the MYI snow samples suggests that MYI regions, in addition to FYI regions, have the potential to play an active role in Arctic boundary layer bromine and chlorine chemistry. The ability of MYI regions to participate in springtime atmospheric halogen chemistry should be considered in regional modeling of halogen activation and interpretation of satellite-based tropospheric bromine monoxide column measurements

Horizontal and vertical structure of reactive bromine events probed by bromine monoxide MAX-DOAS spectroscopy

Heterogeneous photochemistry converts bromide (Br−) to reactive bromine species (Br atoms and bromine monoxide, BrO) that dominate Arctic springtime chemistry. This phenomenon has many impacts such as boundary-layer ozone depletion, mercury oxidation and deposition, and modification of the fate of hydrocarbon species. To study environmental controls on reactive bromine events, the BRomine, Ozone, and Mercury EXperiment (BROMEX) was carried out from early March to mid-April 2012 near Barrow (Utqiaġvik), Alaska. We measured horizontal and vertical gradients in BrO with multiple-axis differential optical absorption spectroscopy (MAX-DOAS) instrumentation at three sites, two mobile and one fixed. During the campaign, a large crack in the sea ice (an open lead) formed pushing one instrument package ∼ 250 km downwind from Barrow (Utqiaġvik). Convection associated with the open lead converted the BrO vertical structure from a surface-based event to a lofted event downwind of the lead influence. The column abundance of BrO downwind of the re-freezing lead was comparable to upwind amounts, indicating direct reactions on frost flowers or open seawater was not a major reactive bromine source. When these three sites were separated by ∼ 30 km length scales of unbroken sea ice, the BrO amount and vertical distributions were highly correlated for most of the time, indicating the horizontal length scales of BrO events were typically larger than ∼ 30 km in the absence of sea ice features. Although BrO amount and vertical distribution were similar between sites most of the time, rapid changes in BrO with edges significantly smaller than this ∼ 30 km length scale episodically transported between the sites, indicating BrO events were large but with sharp edge contrasts. BrO was often found in shallow layers that recycled reactive bromine via heterogeneous reactions on snowpack. Episodically, these surface-based events propagated aloft when aerosol extinction was higher (\u3e 0.1 km−1); however, the presence of aerosol particles aloft was not sufficient to produce BrO aloft. Highly depleted ozone (−1) repartitioned reactive bromine away from BrO and drove BrO events aloft in cases. This work demonstrates the interplay between atmospheric mixing and heterogeneous chemistry that affects the vertical structure and horizontal extent of reactive bromine events

Osteopontin is linked with AKT, FoxO1, and myostatin in skeletal muscle cells

Introduction: Osteopontin (OPN) polymorphisms are associated with muscle size and modify disease progression in Duchenne muscular dystrophy (DMD). We hypothesized that OPN may share a molecular network with myostatin (MSTN). Methods: Studies were conducted in the golden retriever (GRMD) and mdx mouse models of DMD. Follow-up in-vitro studies were employed in myogenic cells and the mdx mouse treated with recombinant mouse (rm) or human (Hu) OPN protein. Results: OPN was increased and MSTN was decreased and levels correlated inversely in GRMD hypertrophied muscle. RM-OPN treatment led to induced AKT1 and FoxO1 phosphorylation, microRNA-486 modulation, and decreased MSTN. An AKT1 inhibitor blocked these effects, whereas an RGD-mutant OPN protein and an RGDS blocking peptide showed similar effects to the AKT inhibitor. RMOPN induced myotube hypertrophy and minimal Feret diameter in mdx muscle. Discussion: OPN may interact with AKT1/MSTN/FoxO1 to modify normal and dystrophic muscle

Changes in Muscle Metabolism are Associated with Phenotypic Variability in Golden Retriever Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is an X-chromosome-linked disorder and the most common monogenic disease in people. Affected boys are diagnosed at a young age, become non-ambulatory by their early teens, and succumb to cardiorespiratory failure by their thirties. Despite being a monogenic condition resulting from mutations in the DMD gene, affected boys have noteworthy phenotypic variability. Efforts have identified genetic modifiers that could modify disease progression and be pharmacologic targets. Dogs affected with golden retriever muscular dystrophy (GRMD) have absent dystrophin and demonstrate phenotypic variability at the functional, histopathological, and molecular level. Our laboratory is particularly interested in muscle metabolism changes in dystrophin-deficient muscle. We identified several metabolic alterations, including myofiber type switching from fast (type II) to slow (type I), reduced glycolytic enzyme expression, reduced and morphologically abnormal mitochondria, and differential AMP-kinase phosphorylation (activation) between hypertrophied and wasted muscle. We hypothesize that muscle metabolism changes are, in part, responsible for phenotypic variability in GRMD. Pharmacological therapies aimed at modulating muscle metabolism can be tested in GRMD dogs for efficacy