Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences

Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

USHA: unified software and hardware architecture for video decoding

Video decoders used in emerging applications need to be flexible to handle a large variety of video formats and deliver scalable performance to handle wide variations in workloads. In this paper we propose a unified software and hardware architecture for video decoding to achieve scalable performance with flexibility. The light weight processor tiles and the reconfigurable hardware tiles in our architecture enable software and hardware implementations to co-exist, while a programmable interconnect enables dynamic interconnection of the tiles. Our process network oriented compilation flow achieves realization agnostic application partitioning and enables seamless migration across uniprocessor, multi-processor, semi hardware and full hardware implementations of a video decoder. An application quality of service aware scheduler monitors and controls the operation of the entire system. We prove the concept through a prototype of the architecture on an off-the-shelf FPGA. The FPGA prototype shows a scaling in performance from QCIF to 1080p resolutions in four discrete steps. We also demonstrate that the reconfiguration time is short enough to allow migration from one configuration to the other without any frame loss.

Strain localization effect on system reliability based design of bridge abutments under earthquake loading

The component and system reliability based design of bridge abutments under earthquake loading is presented in the paper. Planar failure surface has been used in conjunction with pseudo-dynamic approach to compute seismic active earth pressures on an abutment. The pseudo-dynamic method, considers the effect of phase difference in shear waves, soil amplification along with the horizontal seismic accelerations, strain localization in backfill soil and associated post-peak reduction in the shear resistance from peak to residual values along a previously formed failure plane. Four modes of stability viz. sliding, overturning, eccentricity and bearing capacity of the foundation soil are considered in the analysis. The series system reliability is computed with an assumption of independent failure modes. The lower and upper bounds of system reliability are also computed by taking into account the correlations between four failure modes, which is evaluated using the direction cosines of the tangent planes at the most probable points of failure.

Examining the Effectiveness of Discriminant Function Analysis and Cluster Analysis in Species Identification of Male Field Crickets Based on Their Calling Songs

Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and identification.

6PANview: Application performance conscious network monitoring for 6LoWPAN based WSNs

6PANview[1] is a Wireless Sensor Network(WSN) monitoring system for 6LoWPAN/RPL networks which we developed as an overlay network for a WSN application. A monitoring system, while performing its operations for maintaining the health of the monitored network, must also be conscious of its impact on the application performance, and must strive to minimize this impact. To this end, we propose a centralized scheduling algorithm within 6PANview which non-intrusively analyzes application traffic arrival patterns at the base station, identifies network idle periods and schedules monitoring activities. The proposed algorithm finds those periodic sequences which are likely to have given rise to the pattern of arrivals seen at the base station. Parts of those sequences are then extended to coarsely predict future traffic and find epochs where low traffic is predicted, in order to schedule monitoring traffic or other activities at these times. We present simulation results for the proposed prediction and scheduling algorithm and its implementation as part of 6PANview. As an enhancement, we briefly talk about using 6PANview's overlay network architecture for distributed scheduling.

Biomechanics of substrate boring by fig wasps

Female insects of diverse orders bore into substrates to deposit their eggs. Such insects must overcome several biomechanical challenges to successfully oviposit, which include the selection of suitable substrates through which the ovipositor can penetrate without itself fracturing. In many cases, the insect may also need to steer and manipulate the ovipositor within the substrate to deliver eggs at desired locations before rapidly retracting her ovipositor to avoid predation. In the case of female parasitoid ichneumonid wasps, this process is repeated multiple times during her lifetime, thus testing the ability of the ovipositioning apparatus to endure fracture and fatigue. What specific adaptations does the ovipositioning apparatus of a female ichneumonoid wasp possess to withstand these challenges? We addressed this question using a model system composed of parasitoid and pollinator fig wasps. First, we show that parasitoid ovipositor tips have teeth-like structures, preferentially enriched with zinc, unlike the smooth morphology of pollinator ovipositors. We describe sensillae present on the parasitoid ovipositor tip that are likely to aid in the detection of chemical species and mechanical deformations and sample microenvironments within the substrate. Second, using atomic force microscopy, we show that parasitoid tip regions have a higher modulus compared with regions proximal to the abdomen in parasitoid and pollinator ovipositors. Finally, we use videography to film wasps during substrate boring and analyse buckling of the ovipositor to estimate the forces required for substrate boring. Together, these results allow us to describe the biomechanical principles underlying substrate boring in parasitoid ichneumonid wasps. Such studies may be useful for the biomimetic design of surgical tools and in the use of novel mechanisms to bore through hard substrates.

Fully developed thermal transport in combined pressure and electroosmotically driven flow of nanofluid in a microchannel under the effect of a magnetic field

This paper critically analyzes, for the first time, the effect of nanofluid on thermally fully developed magnetohydrodynamic flows through microchannel, by considering combined effects of externally applied pressure gradient and electroosmosis. The classical boundary condition of uniform wall heat flux is considered, and the effects of viscous dissipation as well as Joule heating have been taken into account. Closed-form analytical expressions for the pertinent velocity and temperature distributions and the Nusselt number variations are obtained, in order to examine the role of nanofluids in influencing the fully developed thermal transport in electroosmotic microflows under the effect of magnetic field. Fundamental considerations are invoked to ascertain the consequences of particle agglomeration on the thermophysical properties of the nanofluid. The present theoretical formalism addresses the details of the interparticle interaction kinetics in tune with the pertinent variations in the effective particulate dimensions, volume fractions of the nanoparticles, as well as the aggregate structure of the particulate system. It is revealed that the inclusion of nanofluid changes the transport characteristics and system irreversibility to a considerable extent and can have significant consequences in the design of electroosmotically actuated microfluidic systems.

Continuous vapour adsorption cooling system with three adsorber beds

In this paper, the design of a new solar operated adsorption cooling system with two identical small and one large adsorber beds, which is capable of producing cold continuously, has been proposed. In this system, cold energy is stored in the form of refrigerant in a separate refrigerant storage tank at ambient temperature. Silica gel water is used as a working pair and system is driven by solar energy. The operating principle is described in details and its thermodynamic transient analysis is presented. Effect of COP and SCE for different adsorbent mass and adsorption/desorption time of smaller beds are discussed. Recommended mass and number of cycles of operation for smaller beds to attain continuous cooling with average COP and SCE of 0.63 and 337.5 kJ/kg, respectively are also discussed, at a generation, condenser and evaporator temperatures of 368 K, 303 K and 283 K, respectively. (C) 2015 Elsevier Ltd. All rights reserved.

Load Balancing with Availability Checker and Load Reporters (LB-ACLRs) for improved Performance in Distributed Systems

Distributed system has quite a lot of servers to attain increased availability of service and for fault tolerance. Balancing the load among these servers is an important task to achieve better performance. There are various hardware and software based load balancing solutions available. However there is always an overhead on Servers and the Load Balancer while communicating with each other and sharing their availability and the current load status information. Load balancer is always busy in listening to clients' request and redirecting them. It also needs to collect the servers' availability status frequently, to keep itself up-to-date. Servers are busy in not only providing service to clients but also sharing their current load information with load balancing algorithms. In this paper we have proposed and discussed the concept and system model for software based load balancer along with Availability-Checker and Load Reporters (LB-ACLRs) which reduces the overhead on server and the load balancer. We have also described the architectural components with their roles and responsibilities. We have presented a detailed analysis to show how our proposed Availability Checker significantly increases the performance of the system.

Phytomedicinal importance of Saraca asoca (Ashoka): an exciting past, an emerging present and a promising future

Since the dawn of civilization, natural resources have remained the mainstay of various remedial approaches of humans vis-a-vis a large number of illnesses. Saraca asoca (Roxb.) de Wilde (Saraca indica L.) belonging to the family Caesalpiniaceae has been regarded as a universal panacea in old Indian Ayurvedic texts and has especially been used to manage gynaecological complications and infections besides treating haemmorhagic dysentery, uterine pain, bacterial infections, skin problems, tumours, worm infestations, cardiac and circulatory problems. Almost all parts of the plant are considered pharmacologically valuable. Extensive folkloric practices and ethnobotanical applications of this plant have even lead to the availability of several commercial S. asoca formulations recommended for different indications though adulteration of these remains a pressing concern. Though a wealth of knowledge on this plant is available in both the classical and modern literature, extensive research on its phytomedicinal worth using state-of-the-art tools and methodologies is lacking. Recent reports on bioprospecting of S. asoca endophytic fungi for industrial bioproducts and useful pharmacologically relevant metabolites provide a silver lining to uncover single molecular bio-effectors from its endophytes. Here, we describe socio-ethnobotanical usage, present the current pharmacological status and discuss potential bottlenecks in harnessing the proclaimed phytomedicinal worth of this prescribed Ayurvedic medicinal plant. Finally, we also look into the possible future of the drug discovery and pharmaceutical R&D efforts directed at exploring its pharma legacy.