Discovery of Application Workloads from Network File Traces

An understanding of application I/O access patterns is useful in several situations. First, gaining insight into what applications are doing with their data at a semantic level helps in designing efficient storage systems. Second, it helps create benchmarks that mimic realistic application behavior closely. Third, it enables autonomic systems as the information obtained can be used to adapt the system in a closed loop.All these use cases require the ability to extract the application-level semantics of I/O operations. Methods such as modifying application code to associate I/O operations with semantic tags are intrusive. It is well known that network file system traces are an important source of information that can be obtained non-intrusively and analyzed either online or offline. These traces are a sequence of primitive file system operations and their parameters. Simple counting, statistical analysis or deterministic search techniques are inadequate for discovering application-level semantics in the general case, because of the inherent variation and noise in realistic traces.In this paper, we describe a trace analysis methodology based on Profile Hidden Markov Models. We show that the methodology has powerful discriminatory capabilities that enable it to recognize applications based on the patterns in the traces, and to mark out regions in a long trace that encapsulate sets of primitive operations that represent higher-level application actions. It is robust enough that it can work around discrepancies between training and target traces such as in length and interleaving with other operations. We demonstrate the feasibility of recognizing patterns based on a small sampling of the trace, enabling faster trace analysis. Preliminary experiments show that the method is capable of learning accurate profile models on live traces in an online setting. We present a detailed evaluation of this methodology in a UNIX environment using NFS traces of selected commonly used applications such as compilations as well as on industrial strength benchmarks such as TPC-C and Postmark, and discuss its capabilities and limitations in the context of the use cases mentioned above.

Multiple beam interference of light in an absorbing wedge

Multiple beam interference of light in a wedge is considered when the wedge is filled with an absorbing medium. The aim is to examine a method that may give values of both the real and the imaginary parts of the refractive index of the absorbing medium. We propose here a method to determine these quantities from simple techniques like fringe counting and interferometry, by using as the incident wave either a single Gaussian beam or two parallel Gaussian beams.

Autonomous and non-autonomous traits mediate social cooperation in Dictyostelium discoideum

In the trishanku (triA(-)) mutant of the social amoeba Dictyostelium discoideum, aggregates are smaller than usual and the spore mass is located mid-way up the stalk, not at the apex. We have monitored aggregate territory size, spore allocation and fruiting body morphology in chimaeric groups of (quasi-wild-type) Ax2 and triA(-) cells. Developmental canalisation breaks down in chimaeras and leads to an increase in phenotypic variation. A minority of triA(-) cells causes largely Ax2 aggregation streams to break up; the effect is not due to the counting factor. Most chimaeric fruiting bodies resemble those of Ax2 or triA(-). Others are double-deckers with a single stalk and two spore masses, one each at the terminus and midway along the stalk. The relative number of spores belonging to the two genotypes depends both on the mixing ratio and on the fruiting body morphology. In double-deckers formed from 1:1 chimaeras, the upper spore mass has more Ax2 spores, and the lower spore mass more triA(-) spores, than expected. Thus, the traits under study depend partly on the cells' own genotype and partly on the phenotypes, and so genotypes, of other cells: they are both autonomous and non-autonomous. These findings strengthen the parallels between multicellular development and behaviour in social groups. Besides that, they reinforce the point that a trait can be associated with a genotype only in a specified context.

A unified view of the Apriori-based algorithms for frequent episode discovery

Frequent episode discovery framework is a popular framework in temporal data mining with many applications. Over the years, many different notions of frequencies of episodes have been proposed along with different algorithms for episode discovery. In this paper, we present a unified view of all the apriori-based discoverymethods for serial episodes under these different notions of frequencies. Specifically, we present a unified view of the various frequency counting algorithms. We propose a generic counting algorithm such that all current algorithms are special cases of it. This unified view allows one to gain insights into different frequencies, and we present quantitative relationships among different frequencies.Our unified view also helps in obtaining correctness proofs for various counting algorithms as we show here. It also aids in understanding and obtaining the anti-monotonicity properties satisfied by the various frequencies, the properties exploited by the candidate generation step of any apriori-based method. We also point out how our unified view of counting helps to consider generalization of the algorithm to count episodes with general partial orders.

Fast algorithms for frequent episode discovery in event sequences

In this paper we consider the process of discovering frequent episodes in event sequences. The most computationally intensive part of this process is that of counting the frequencies of a set of candidate episodes. We present two new frequency counting algorithms for speeding up this part. These, referred to as non-overlapping and non-inteleaved frequency counts, are based on directly counting suitable subsets of the occurrences of an episode. Hence they are different from the frequency counts of Mannila et al [1], where they count the number of windows in which the episode occurs. Our new frequency counts offer a speed-up factor of 7 or more on real and synthetic datasets. We also show how the new frequency counts can be used when the events in episodes have time-durations as well.

A unified view of the apriori-based algorithms for frequent episode discovery

Frequent episode discovery framework is a popular framework in temporal data mining with many applications. Over the years, many different notions of frequencies of episodes have been proposed along with different algorithms for episode discovery. In this paper, we present a unified view of all the apriori-based discovery methods for serial episodes under these different notions of frequencies. Specifically, we present a unified view of the various frequency counting algorithms. We propose a generic counting algorithm such that all current algorithms are special cases of it. This unified view allows one to gain insights into different frequencies, and we present quantitative relationships among different frequencies. Our unified view also helps in obtaining correctness proofs for various counting algorithms as we show here. It also aids in understanding and obtaining the anti-monotonicity properties satisfied by the various frequencies, the properties exploited by the candidate generation step of any apriori-based method. We also point out how our unified view of counting helps to consider generalization of the algorithm to count episodes with general partial orders.

Study on the detection efficiency of gaseous photomultipliers

Efficient photon detection in gaseous photomultipliers require maximum photoelectron yield from the photocathode surface and also detection of them. In this work we have investigated the parameters that affect the photoelectron yield from the photocathode surface and methods to improve them thus ensuring high detection efficiency of the gaseous photomultiplier. The parameters studied are the electric field at the photocathode surface, surface properties of photocathode and pressure of gas mixture inside the gaseous photomultiplier. It was observed that optimized electric field at the photocathode ensures high detection efficiency. Lower pressure of filled gas increases the photoelectron yield from the photocathode surface but reduces the focusing probability of electrons inside the electron multiplier. Also evacuation for longer duration before gas filling increases the photoelectron yield.

MRT Letter: Light Sheet Based Imaging Flow Cytometry on a Microfluidic Platform

We propose a light sheet based imaging flow cytometry technique for simultaneous counting and imaging of cells on a microfluidic platform. Light sheet covers the entire microfluidic channel and thus omits the necessity of flow focusing and point scanning based technology. Another advantage lies in the orthogonal detection geometry that totally cuts-off the incident light, thereby substantially reducing the background in the detection. Compared to the existing state-of-art techniques the proposed technique shows marked improvement. Using fluorescently-coated Saccharomyces cerevisiae cells we have recorded cell counting with throughput as high as 2,090 cells/min in the low flow rate regime and were able to image the individual cells on-the-go. Overall, the proposed system is cost-effective and simple in channel geometry with the advantage of efficient counting in operational regime of low laminar flow. This technique may advance the emerging field of microfluidic based cytometry for applications in nanomedicine and point of care diagnostics. Microsc. Res. Tech. 76:1101-1107, 2013. (c) 2013 Wiley Periodicals, Inc.

Nodal domains of the equilateral triangle billiard

We characterize the eigenfunctions of an equilateral triangle billiard in terms of its nodal domains. The number of nodal domains has a quadratic form in terms of the quantum numbers, with a non-trivial number-theoretic factor. The patterns of the eigenfunctions follow a group-theoretic connection in a way that makes them predictable as one goes from one state to another. Extensive numerical investigations bring out the distribution functions of the mode number and signed areas. The statistics of the boundary intersections is also treated analytically. Finally, the distribution functions of the nodal loop count and the nodal counting function are shown to contain information about the classical periodic orbits using the semiclassical trace formula. We believe that the results belong generically to non-separable systems, thus extending the previous works which are concentrated on separable and chaotic systems.

Trans-spliced Heat Shock Protein 90 Modulates Encystation in Giardia lamblia

Background: Hsp90 from Giardia lamblia is expressed by splicing of two independently transcribed RNA molecules, coded by genes named HspN and HspC located 777 kb apart. The reasons underlying such unique trans-splicing based generation of GlHsp90 remain unclear. Principle Finding: In this study using mass-spectrometry we identify the sequence of the unique, junctional peptide contributed by the 5' UTR of HspC ORF. This peptide is critical for the catalytic function of Hsp90 as it harbours an essential ``Arg'' in its sequence. We also show that full length GlHsp90 possesses all the functional hall marks of a canonical Hsp90 including its ability to bind and hydrolyze ATP. Using qRT-PCR as well as western blotting approach we find the reconstructed Hsp90 to be induced in response to heat shock. On the contrary we find GlHsp90 to be down regulated during transition from proliferative trophozoites to environmentally resistant cysts. This down regulation of GlHsp90 appears to be mechanistically linked to the encystation process as we find pharmacological inhibition of GlHsp90 function to specifically induce encystation. Significance: Our results implicate the trans-spliced GlHsp90 from Giardia lamblia to regulate an essential stage transition in the life cycle of this important human parasite.

High resolution light-sheet based high-throughput imaging cytometry system enables visualization of intra-cellular organelles

Visualization of intracellular organelles is achieved using a newly developed high throughput imaging cytometry system. This system interrogates the microfluidic channel using a sheet of light rather than the existing point-based scanning techniques. The advantages of the developed system are many, including, single-shot scanning of specimens flowing through the microfluidic channel at flow rate ranging from micro-to nano- lit./min. Moreover, this opens-up in-vivo imaging of sub-cellular structures and simultaneous cell counting in an imaging cytometry system. We recorded a maximum count of 2400 cells/min at a flow-rate of 700 nl/min, and simultaneous visualization of fluorescently-labeled mitochondrial network in HeLa cells during flow. The developed imaging cytometry system may find immediate application in biotechnology, fluorescence microscopy and nano-medicine. (C) 2014 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Logarithmic corrections to extremal black hole entropy in N=2, 4 and 8 supergravity

We compute the logarithmic correction to black hole entropy about exponentially suppressed saddle points of the Quantum Entropy Function corresponding to Z(N) orbifolds of the near horizon geometry of the extremal black hole under study. By carefully accounting for zero mode contributions we show that the logarithmic contributions for quarter-BPS black holes in N = 4 supergravity and one-eighth BPS black holes in N = 8 supergravity perfectly match with the prediction from the microstate counting. We also find that the logarithmic contribution for half-BPS black holes in N = 2 supergravity depends non-trivially on the Z(N) orbifold. Our analysis draws heavily on the results we had previously obtained for heat kernel coefficients on Z(N) orbifolds of spheres and hyperboloids in arXiv:1311.6286 and we also propose a generalization of the Plancherel formula to Z(N) orbifolds of hyperboloids to an expression involving the Harish-Chandra character of sl (2, R), a result which is of possible mathematical interest.

Heat kernels on the AdS(2) cone and logarithmic corrections to extremal black hole entropy

We develop new techniques to efficiently evaluate heat kernel coefficients for the Laplacian in the short-time expansion on spheres and hyperboloids with conical singularities. We then apply these techniques to explicitly compute the logarithmic contribution to black hole entropy from an N = 4 vector multiplet about a Z(N) orbifold of the near-horizon geometry of quarter-BPS black holes in N = 4 supergravity. We find that this vanishes, matching perfectly with the prediction from the microstate counting. We also discuss possible generalisations of our heat kernel results to higher-spin fields over ZN orbifolds of higher-dimensional spheres and hyperboloids.

Whole exome sequencing in an Indian family links Coats plus syndrome and dextrocardia with a homozygous novel CTC1 and a rare HES7 variation

Background: Coats plus syndrome is an autosomal recessive, pleiotropic, multisystem disorder characterized by retinal telangiectasia and exudates, intracranial calcification with leukoencephalopathy and brain cysts, osteopenia with predisposition to fractures, bone marrow suppression, gastrointestinal bleeding and portal hypertension. It is caused by compound heterozygous mutations in the CTC1 gene. Case presentation: We encountered a case of an eight-year old boy from an Indian family with manifestations of Coats plus syndrome along with an unusual occurrence of dextrocardia and situs inversus. Targeted resequencing of the CTC1 gene as well as whole exome sequencing (WES) were conducted in this family to identify the causal variations. The identified candidate variations were screened in ethnicity matched healthy controls. The effect of CTC1 variation on telomere length was assessed using Southern blot. A novel homozygous missense mutation c.1451A > C (p.H484P) in exon 9 of the CTC1 gene and a rare 3'UTR known dbSNP variation (c.*556 T > C) in HES7 were identified as the plausible candidates associated with this complex phenotype of Coats plus and dextrocardia. This CTC1 variation was absent in the controls and we also observed a reduced telomere length in the affected individual's DNA, suggesting its likely pathogenic nature. The reported p.H484P mutation is located in the N-terminal 700 amino acid regionthat is important for the binding of CTC1 to ssDNA through its two OB domains. WES data also showed a rare homozygous missense variation in the TEK gene in the affected individual. Both HES7 and TEK are targets of the Notch signaling pathway. Conclusions: This is the first report of a genetically confirmed case of Coats plus syndrome from India. By means of WES, the genetic variations in this family with unique and rare complex phenotype could be traced effectively. We speculate the important role of Notch signaling in this complex phenotypic presentation of Coats plus syndrome and dextrocardia. The present finding will be useful for genetic diagnosis and carrier detection in the family and for other patients with similar disease manifestations.

Porous membranes designed from bi-phasic polymeric blends containing silver decorated reduced graphene oxide synthesized via a facile one-pot approach

In this work, porous membranes were designed by selectively etching the PEO phase, by water, from a melt-mixed PE/PEO blend. The pure water flux and the resistance across the membrane were systematically evaluated by employing an indigenously developed cross flow membrane setup. Both the phase morphology and the cross sectional morphology of the membranes was assessed by scanning electron microscopy and an attempt was made to correlate the observed morphology with the membrane performance. In order to design antibacterial membranes for water purification, partially reduced graphene oxide (rGO), silver nanoparticles (Ag) and silver nanoparticles decorated with rGO (rGO-Ag) were synthesized and incorporated directly into the blends during melt mixing. The loss of viability of bacterial cells was determined by the colony counting method using E. coli as a model bacterium. SEM images display that the direct contact with the rGO-Ag nanoparticles disrupts the cell membrane. In addition, the rGO-Ag nanoparticles exhibited a synergistic effect with respect to bacterial cell viability in comparison to both rGO and Ag nanoparticles. The possible mechanism associated with the antibacterial activity in the membranes was discussed. This study opens new avenues in designing antibacterial membranes for water purification.