Elastic Resources Framework in IaaS, preserving performance SLAs

Elasticity in cloud systems provides the flexibility to acquire and relinquish computing resources on demand. However, in current virtualized systems resource allocation is mostly static. Resources are allocated during VM instantiation and any change in workload leading to significant increase or decrease in resources is handled by VM migration. Hence, cloud users tend to characterize their workloads at a coarse grained level which potentially leads to under-utilized VM resources or under performing application. A more flexible and adaptive resource allocation mechanism would benefit variable workloads, such as those characterized by web servers. In this paper, we present an elastic resources framework for IaaS cloud layer that addresses this need. The framework provisions for application workload forecasting engine, that predicts at run-time the expected demand, which is input to the resource manager to modulate resource allocation based on the predicted demand. Based on the prediction errors, resources can be over-allocated or under-allocated as compared to the actual demand made by the application. Over-allocation leads to unused resources and under allocation could cause under performance. To strike a good trade-off between over-allocation and under-performance we derive an excess cost model. In this model excess resources allocated are captured as over-allocation cost and under-allocation is captured as a penalty cost for violating application service level agreement (SLA). Confidence interval for predicted workload is used to minimize this excess cost with minimal effect on SLA violations. An example case-study for an academic institute web server workload is presented. Using the confidence interval to minimize excess cost, we achieve significant reduction in resource allocation requirement while restricting application SLA violations to below 2-3%.

Efficient QR Decomposition Using Low Complexity Column-wise Givens Rotation (CGR)

QR decomposition (QRD) is a widely used Numerical Linear Algebra (NLA) kernel with applications ranging from SONAR beamforming to wireless MIMO receivers. In this paper, we propose a novel Givens Rotation (GR) based QRD (GR QRD) where we reduce the computational complexity of GR and exploit higher degree of parallelism. This low complexity Column-wise GR (CGR) can annihilate multiple elements of a column of a matrix simultaneously. The algorithm is first realized on a Two-Dimensional (2 D) systolic array and then implemented on REDEFINE which is a Coarse Grained run-time Reconfigurable Architecture (CGRA). We benchmark the proposed implementation against state-of-the-art implementations to report better throughput, convergence and scalability.

Bi-Modal DRAM Cache: Improving Hit Rate, Hit Latency and Bandwidth

In this paper, we present Bi-Modal Cache - a flexible stacked DRAM cache organization which simultaneously achieves several objectives: (i) improved cache hit ratio, (ii) moving the tag storage overhead to DRAM, (iii) lower cache hit latency than tags-in-SRAM, and (iv) reduction in off-chip bandwidth wastage. The Bi-Modal Cache addresses the miss rate versus off-chip bandwidth dilemma by organizing the data in a bi-modal fashion - blocks with high spatial locality are organized as large blocks and those with little spatial locality as small blocks. By adaptively selecting the right granularity of storage for individual blocks at run-time, the proposed DRAM cache organization is able to make judicious use of the available DRAM cache capacity as well as reduce the off-chip memory bandwidth consumption. The Bi-Modal Cache improves cache hit latency despite moving the metadata to DRAM by means of a small SRAM based Way Locator. Further by leveraging the tremendous internal bandwidth and capacity that stacked DRAM organizations provide, the Bi-Modal Cache enables efficient concurrent accesses to tags and data to reduce hit time. Through detailed simulations, we demonstrate that the Bi-Modal Cache achieves overall performance improvement (in terms of Average Normalized Turnaround Time (ANTT)) of 10.8%, 13.8% and 14.0% in 4-core, 8-core and 16-core workloads respectively.

On Fast Bilateral Filtering Using Fourier Kernels

It was demonstrated in earlier work that, by approximating its range kernel using shiftable functions, the nonlinear bilateral filter can be computed using a series of fast convolutions. Previous approaches based on shiftable approximation have, however, been restricted to Gaussian range kernels. In this work, we propose a novel approximation that can be applied to any range kernel, provided it has a pointwise-convergent Fourier series. More specifically, we propose to approximate the Gaussian range kernel of the bilateral filter using a Fourier basis, where the coefficients of the basis are obtained by solving a series of least-squares problems. The coefficients can be efficiently computed using a recursive form of the QR decomposition. By controlling the cardinality of the Fourier basis, we can obtain a good tradeoff between the run-time and the filtering accuracy. In particular, we are able to guarantee subpixel accuracy for the overall filtering, which is not provided by the most existing methods for fast bilateral filtering. We present simulation results to demonstrate the speed and accuracy of the proposed algorithm.

Dynamic path profile aided recompilation in a JAVA just-in-time compiler

Just-in-Time (JIT) compilers for Java can be augmented by making use of runtime profile information to produce better quality code and hence achieve higher performance. In a JIT compilation environment, the profile information obtained can be readily exploited in the same run to aid recompilation and optimization of frequently executed (hot) methods. This paper discusses a low overhead path profiling scheme for dynamically profiling AT produced native code. The profile information is used in recompilation during a subsequent invocation of the hot method. During recompilation tree regions along the hot paths are enlarged and instruction scheduling at the superblock level is performed. We have used the open source LaTTe AT compiler framework for our implementation. Our results on a SPARC platform for SPEC JVM98 benchmarks indicate that (i) there is a significant reduction in the number of tree regions along the hot paths, and (ii) profile aided recompilation in LaTTe achieves performance comparable to that of adaptive LaTTe in spite of retranslation and profiling overheads.

Traffic Profiling for Efficient Network Resource Utilization.

Traffic Engineering has been the prime concern for Internet Service Providers (ISPs), with the main focus being minimization of over-utilization of network capacity even though additional capacity is available which is under-utilized, Furthermore, requirements of timely delivery of digitized audiovisual information raises a new challenge of finding a path meeting these requirements. This paper addresses the issue of (a) distributing load to achieve global efficiency in resource utilization. (b) Finding a path satisfying the real time requirements of, delay and bandwidth requested by the applications. In this paper we do a critical study of the link utilization that varies over time and determine the time interval during which the link occupancy remains constant across days. This information helps in pre-determining link utilization that is useful in balancing load in the network Finally, we run simulations that use a dynamic time interval for profiling traffic and show improvement in terms number of calls admitted/blocked.

Rise Time of a Surface-Acoustic-Wave Resonator

This paper presents the results of the rise time calculation of a SAW resonator. The total rise time is given by rise time = [(rise time of cavity)2 + (rise time of reflectors)2 + (rise time of IDT) 2 ]. 1/2 These rise times are calculated in terms of the effective length of the cavity , the characteristics of the reflector, and the number of finger pairs in the IDT. The rise time of a 38 MHz one-port resonator on Y-Z LiNb03 calculated using this approach is found to be in good agreement with experimental results .

Bounding Run-Times of Local Adiabatic Algorithms

A common trick for designing faster quantum adiabatic algorithms is to apply the adiabaticity condition locally at every instant. However it is often difficult to determine the instantaneous gap between the lowest two eigenvalues, which is an essential ingredient in the adiabaticity condition. In this paper we present a simple linear algebraic technique for obtaining a lower bound on the instantaneous gap even in such a situation. As an illustration, we investigate the adiabatic un-ordered search of van Dam et al. [17] and Roland and Cerf [15] when the non-zero entries of the diagonal final Hamiltonian are perturbed by a polynomial (in log N, where N is the length of the unordered list) amount. We use our technique to derive a bound on the running time of a local adiabatic schedule in terms of the minimum gap between the lowest two eigenvalues.

Genome-wide expression profiling identifies deregulated miRNAs in malignant astrocytoma

Malignant astrocytoma includes anaplastic astrocytoma (grade III) and glioblastoma (grade IV). Among them, glioblastoma is the most common primary brain tumor with dismal responses to all therapeutic modalities. We performed a large-scale, genome-wide microRNA (miRNA) (n=756) expression profiling of 26 glioblastoma, 13 anaplastic astrocytoma and 7 normal brain samples with an aim to find deregulated miRNA in malignant astrocytoma. We identified several differentially regulated miRNAs between these groups, which could differentiate glioma grades and normal brain as recognized by PCA. More importantly, we identified a most discriminatory 23-miRNA expression signature, by using PAM, which precisely distinguished glioblastoma from anaplastic astrocytoma with an accuracy of 95%. The differential expression pattern of nine miRNAs was further validated by real-time RT-PCR on an independent set of malignant astrocytomas (n-72) and normal samples (n=7). Inhibition of two glioblastoma-upregulated miRNAs (miR-21 and miR-23a) and exogenous overexpression of two glioblastoma-downregulated miRNAs (miR-218 and miR-219-5p) resulted in reduced soft agar colony formation but showed varying effects on cell proliferation and chemosensitivity. Thus we have identified the miRNA expression signature for malignant astrocytoma, in particular glioblastoma, and showed the miRNA involvement and their importance in astrocytoma development. Modern Pathology (2010) 23, 1404-1417; doi:10.1038/modpathol.2010.135; published online 13 August 2010

Apparatus and method for heat-run test on high-power PWM converters with low energy expenditure

Before installation, a voltage source converter is usually subjected to heat-run test to verify its thermal design and performance under load. For heat-run test, the converter needs to be operated at rated voltage and rated current for a substantial length of time. Hence, such tests consume huge amount of energy in case of high-power converters. Also, the capacities of the source and loads available in the research and development (R&D) centre or the production facility could be inadequate to conduct such tests. This paper proposes a method to conduct heat-run tests on high-power, pulse width modulated (PWM) converters with low energy consumption. The experimental set-up consists of the converter under test and another converter (of similar or higher rating), both connected in parallel on the ac side and open on the dc side. Vector-control or synchronous reference frame control is employed to control the converters such that one draws certain amount of reactive power and the other supplies the same; only the system losses are drawn from the mains. The performance of the controller is validated through simulation and experiments. Experimental results, pertaining to heat-run tests on a high-power PWM converter, are presented at power levels of 25 kVA to 150 kVA.

How to run a campaign: Optimal control of SIS and SIR information epidemics

Information spreading in a population can be modeled as an epidemic. Campaigners (e.g., election campaign managers, companies marketing products or movies) are interested in spreading a message by a given deadline, using limited resources. In this paper, we formulate the above situation as an optimal control problem and the solution (using Pontryagin's Maximum Principle) prescribes an optimal resource allocation over the time of the campaign. We consider two different scenarios-in the first, the campaigner can adjust a direct control (over time) which allows her to recruit individuals from the population (at some cost) to act as spreaders for the Susceptible-Infected-Susceptible (SIS) epidemic model. In the second case, we allow the campaigner to adjust the effective spreading rate by incentivizing the infected in the Susceptible-Infected-Recovered (SIR) model, in addition to the direct recruitment. We consider time varying information spreading rate in our formulation to model the changing interest level of individuals in the campaign, as the deadline is reached. In both the cases, we show the existence of a solution and its uniqueness for sufficiently small campaign deadlines. For the fixed spreading rate, we show the effectiveness of the optimal control strategy against the constant control strategy, a heuristic control strategy and no control. We show the sensitivity of the optimal control to the spreading rate profile when it is time varying. (C) 2014 Elsevier Inc. All rights reserved.

Profiling of Luteal Transcriptome during Prostaglandin F2-Alpha Treatment in Buffalo Cows: Analysis of Signaling Pathways Associated with Luteolysis

In several species including the buffalo cow, prostaglandin (PG) F-2 alpha is the key molecule responsible for regression of corpus luteum (CL). Experiments were carried out to characterize gene expression changes in the CL tissue at various time points after administration of luteolytic dose of PGF(2 alpha) in buffalo cows. Circulating progesterone levels decreased within 1 h of PGF(2 alpha) treatment and evidence of apoptosis was demonstrable at 18 h post treatment. Microarray analysis indicated expression changes in several of immediate early genes and transcription factors within 3 h of treatment. Also, changes in expression of genes associated with cell to cell signaling, cytokine signaling, steroidogenesis, PG synthesis and apoptosis were observed. Analysis of various components of LH/CGR signaling in CL tissues indicated decreased LH/CGR protein expression, pCREB levels and PKA activity post PGF(2 alpha) treatment. The novel finding of this study is the down regulation of CYP19A1 gene expression accompanied by decrease in expression of E-2 receptors and circulating and intra luteal E-2 post PGF(2 alpha) treatment. Mining of microarray data revealed several differentially expressed E-2 responsive genes. Since CYP19A1 gene expression is low in the bovine CL, mining of microarray data of PGF(2 alpha)-treated macaques, the species with high luteal CYP19A1 expression, showed good correlation between differentially expressed E-2 responsive genes between both the species. Taken together, the results of this study suggest that PGF(2 alpha) interferes with luteotrophic signaling, impairs intraluteal E-2 levels and regulates various signaling pathways before the effects on structural luteolysis are manifest.

Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation

Background. Pediatric glioblastoma multiforme (GBM) is rare, and there is a single study, a seminal discovery showing association of histone H3.3 and isocitrate dehydrogenase (IDH) 1 mutation with a DNA methylation signature. The present study aims to validate these findings in an independent cohort of pediatric GBM, compare it with adult GBM, and evaluate the involvement of important functionally altered pathways. Methods. Genome-wide methylation profiling of 21 pediatric GBM cases was done and compared with adult GBM data (GSE22867). We performed gene mutation analysis of IDH1 and H3 histone family 3A (H3F3A), status evaluation of glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP), and Gene Ontology analysis. Experimental evaluation of reactive oxygen species (ROS) association was also done. Results. Distinct differences were noted between methylomes of pediatric and adult GBM. Pediatric GBM was characterized by 94 hypermethylated and 1206 hypomethylated cytosine-phosphate-guanine (CpG) islands, with 3 distinct clusters, having a trend to prognostic correlation. Interestingly, none of the pediatric GBM cases showed G-CIMP/IDH1 mutation. Gene Ontology analysis identified ROS association in pediatric GBM, which was experimentally validated. H3F3A mutants (36.4%; all K27M) harbored distinct methylomes and showed enrichment of processes related to neuronal development, differentiation, and cell-fate commitment. Conclusions. Our study confirms that pediatric GBM has a distinct methylome compared with that of adults. Presence of distinct clusters and an H3F3A mutation-specific methylome indicate existence of epigenetic subgroups within pediatric GBM. Absence of IDH1/G-CIMP status further indicates that findings in adult GBM cannot be simply extrapolated to pediatric GBM and that there is a strong need for identification of separate prognostic markers. A possible role of ROS in pediatric GBM pathogenesis is demonstrated for the first time and needs further evaluation.

Differential proteomic and genomic profiling of mouse striatal cell model of Huntington's disease and control; probable implications to the disease biology

Huntington's disease (HD) is an autosomal dominant disorder of central nervous system caused by expansion of CAG repeats in exon1 of the huntingtin gene (Htt). Among various dysfunctions originated from the mutation in Htt gene, transcriptional deregulation has been considered to be one of the most important abnormalities. Large numbers of investigations identified altered expressions of genes in brains of HD patients and many models of HD. In this study we employed 2D SDS-PAGE/MALDI-MS coupled with 2D-DIGE and real-time PCR experiments of an array of genes focused to HD pathway to determine altered protein and gene expressions in STHdh(Q111)/Hdh(Q111) cells, a cell model of HD and compared with STHdh(Q7)/Hdh(Q7) cells, its wild type counterpart. We annotated 76 proteins from these cells and observed differential expressions of 31 proteins (by 2D-DIGE) involved in processes like unfolded protein binding, negative regulation of neuron apoptosis, response to superoxides etc. Our PCR array experiments identified altered expressions of 47 genes. Altogether significant alteration of 77 genes/proteins could be identified in this HD cell line with potential relevance to HD biology. Biological significance: In this study we intended to find out differential proteomic and genomic profiles in HD condition. We used the STHdh cells, a cellular model for HD and control. These are mouse striatal neuronal cell lines harboring 7 and 111 knock -in CAG repeats in their two alleles. The 111Q containing cell line (STHdh(Q111)/Hdh(Q111)) mimics diseased condition, whereas the 7Q containing ones (STHdh(Q7)/Hdh(Q7)), serves as the proper control cell line. Proteomic experiments were performed earlier to obtain differential expressions of proteins in R6/2 mice models, Hdh(Q) knock -in mice and in plasma and CSF from HD patients. However, no earlier report on proteomic alterations in these two HD cell lines and control was available in literature. It was, therefore, an important objective to find out differential expressions of proteins in these two cell lines. In this study, we annotated 76 proteins from STHdh(Q7)/Hdh(Q7) and STHdh(Q111)/Hdh(Q111) cells using 2D-gel/mass spectrometry. Next, by performing 2D-DIGE, we observed differential expressions of 31 proteins (16 upregulated and 15 downregulated) between these two cell lines. We also performed customized qRT-PCR array focused to HD pathway and found differential expressions of 47 genes (8 gene exptessions increased and 39 genes were decreased significantly). A total of 77 genes/proteins (Htt downregulated in both the studies) were found to be significantly altered from both the experimental paradigms. We validated the differential expressions of Vim, Hypk, Ran, Dstn, Hspa5 and Sod2 either by qRT-PCR or Western blot analysis or both. Out of these 77, similar trends in alteration of 19 out of 31 and 38 out of 47 proteins/genes were reported in earlier studies. Thus our study confirmed earlier observations on differential gene/protein expressions in HD and are really useful. Additionally, we observed differential expression of some novel genes/proteins. One of this was Hypk, a Htt-interacting chaperone protein with the ability to solubilize mHtt aggregated structures in cell lines. We propose that downregulation of Hypk in STHdh-Qm (Q111)/Hdh(Q111) has a causal effect towards HD pathogenesis. Thus the novel findings from our study need further research and might be helpful to understand the molecular mechanism behind HD pathogenesis. (C) 2015 Elsevier B.V. All rights reserved.