Bead-based polymerase chain reaction on a microchip

We present a bead-based approach to microfluidic polymerase chain reaction (PCR), enabling fluorescent detection and sample conditioning in a single microchamber. Bead-based PCR, while not extensively investigated in microchip format, has been used in a variety of bioanalytical applications in recent years. We leverage the ability of bead-based PCR to accumulate fluorescent labels following DNA amplification to explore a novel DNA detection scheme on a microchip. The microchip uses an integrated microheater and temperature sensor for rapid control of thermal cycling temperatures, while the sample is held in a microchamber fabricated from (poly)dimethylsiloxane and coated with Parylene. The effects of key bead-based PCR parameters, including annealing temperature and concentration of microbeads in the reaction mixture, are studied to achieve optimized device sensitivity and detection time. The device is capable of detecting a synthetically prepared section of the Bordetella pertussis genome in as few as 10 temperature cycles with times as short as 15?min. We then demonstrate the use of the procedure in an integrated device; capturing, amplifying, detecting, and purifying template DNA in a single microfluidic chamber. These results show that this method is an effective method of DNA detection which is easily integrated in a microfluidic device to perform additional steps such as sample pre-conditioning.     

A Distributed Address Configuration Scheme for a MANET

This paper proposes a distributed address configuration scheme for a Mobile Ad hoc Network (MANET). The architecture for a MANET, the algorithm of constructing a MANET, and the algorithm for calculating a unique address space for the assignment are proposed. In the architecture, a common node has a unique address space for the assignment, and an isolated node can acquire a unique address from a neighboring common node without performing duplicate address detection. In this way, the address configuration task is distributed around common nodes. In this scheme, the control packets used for address configuration are exchanged within a one-hop scope, so the scalability is enhanced. This paper also presents an address recovery algorithm that can effectively retrieve the address resources released by failed nodes and the MANET merging/partitioning algorithm that can ensure a node’s address uniqueness. This paper compares the performance parameters of the proposed scheme and the existing schemes, including strong duplicate address detection and prime dynamic host configuration protocol, and the comparative results show that the address configuration cost of the proposed scheme is lower and the delay is shorter.     

Nafion-film-based micro–nanofluidic device for concurrent DNA preconcentration and separation in free solution

This paper presents a Nafion-film-based micro–nanofluidic device for concurrent DNA preconcentration and separation. The principle of the device is based on the combination of (a) ion concentration polarization phenomenon at the junction of the microchannel and the nanochannels in the Nafion film to form opposing electrophoretic and electroosmotic forces acting on the DNAs and (b) end-labeled-free solution electrophoresis to harness the charge-to-mass ratio for molecular differentiation. The experiments successfully demonstrated concurrent preconcentration and separation of DNA mixture in free solution within 240 s, yielding concentration ratios up to 1,150× and separation resolution of 1.85. The effect of applied electric field on the concentration and separation performance was also investigated. The device can be used as a key sample preparation element in conjunction with micro- or nano-fluidic sensors for microTAS functionality.     

A Substitution Based Model for the Implementation of PROLOG——The Design and Implementation of LPROLOG

Since PROLOG has been chosen as the Fifth Generation Computer's Kernal Language,it ispresently one of the hottest topics among computer scientists all over the world.Recently,theimplementation technique and the application of PROLOG have been developed rapidly.In thispaper,a new implementation scheme for PROLOG is proposed.The scheme is based on thesubstitution of instantiated veriable values.It has many advantages,such as a higher runningspeed,less main memory requirement,and easier to be implemented.The scheme has beenimplemented by the authors on IBM4341.     

An efficient mutual authentication RFID scheme based on elliptic curve cryptography

Radio frequency identification (RFID) tags have been widely deployed in many applications, such as supply chain management, inventory control, and traffic card payment. However, these applications can suffer from security issues or privacy violations when the underlying data-protection techniques are not properly designed. Hence, many secure RFID authentication protocols have been proposed. According to the resource usage of the tags, secure RFID protocols are classified into four types: full-fledged, simple, lightweight, and ultra-lightweight. In general, non-full-fledged protocols are vulnerable to desynchronization, impersonation, and tracking attacks, and they also lack scalability. If the tag resources allow more flexibility, full-fledged protocols seem to be an attractive solution. In this study, we examine full-fledged RFID authentication protocols and discuss their security issues. We then design a novel RFID authentication protocol based on elliptic curve cryptography, to avoid these issues. In addition, we present a detailed security analysis and a comparison with related studies; the results show that our scheme is more resistant to a variety of attacks and that it has the best scalability, while maintaining competitive levels of efficiency.     

Quantitative steganalysis of spatial ±1 steganography in JPEG decompressed images

On the basis of the analysis of JPEG error and stegonoise, we propose a novel quantitative steganalyzer for spatial ±1 steganography in JPEG decompressed images. First, we present a particular theoretical argument that the cover images, which are originally stored in JPEG format, can be approximately estimated through JPEG recompression with the detected quantization table. Then, on the basis of the relationship between the message embedding rate and the variance of the stegonoise in the discrete cosine transformation (DCT) domain, we construct a polynomial regression model to estimate the secret message length. The extensive experimental results show that the proposed scheme is computationally feasible and that it significantly outperforms the existing state-of-the-art estimators, especially for the images with high quality factors and embedding rates. The order of magnitude of the prediction error using the proposed scheme can remain in the 10^?4 range, as measured by the median absolute difference. Moreover, our estimator is stable and robust with respect to the embedding rate and quality factor.     

Cryptanalysis and improvement of an efficient mutual authentication RFID scheme based on elliptic curve cryptography

Radio frequency identification (RFID) is a wireless technology for automatic identification and data capture. Security and privacy issues in the RFID systems have attracted much attention. Many approaches have been proposed to achieve the security and privacy goals. One of these approaches is RFID authentication protocols by which a server and tags can authorize each other through an intracity process. Recently, Chou proposed a RFID authentication protocol based on elliptic curve cryptography. However, this paper demonstrates that the Chou’s protocol does not satisfy tag privacy, forward privacy and authentication, and server authentication. Based on these security and privacy problems, we also show that Chou’s protocol is defenseless to impersonation attacks, tag cloning attacks and location tracking attacks. Therefore, we propose a more secure and efficient scheme, which does not only cover all the security flaws and weaknesses of related previous protocols, but also provides more functionality. We prove the security of the proposed improved protocol in the random oracle model.     

A heuristic method for solving integer-valued decompositional multiindex problems

We consider NP-hard integer-valued multiindex problems of transportation type. We distinguish a subclass of polynomially solvable multiindex problems, namely multiindex problems with decomposition structure. We construct a general scheme for a heuristic method to solve a number of similar NP-hard decompositional multiindex problems. For one version of implementation for this scheme, we estimate its deviation from the optimum. We illustrate our results with the example of designing a class schedule.     

Operating regimes of a magnetic split-flow thin (SPLITT) fractionation microfluidic device for immunomagnetic separation

Magnetic bead-based immunoassays in the microfluidic format have attracted particular interest as it has several advantages over other microfluidic separation techniques. Magnetic split-flow thin fractionation (SPLITT) is a compact version of microfluidic sorting where a bidispersed or polydispersed suspension of magnetic particle–analyte conjugates can be selectively isolated into co-flowing streams of nearly monodispersed particles. Although the device offers capability of identifying and separating more than one target analytes simultaneously, its performance is sensitive to the slightest variation of the operating condition. Herein, we have numerically investigated the performance of a microscale magnetic SPLITT device. Using a coupled Eulerian–Lagrangian approach, we have evaluated the capture efficiency (CE) and separation index (SI) for each particle type collected at their designated outlet of the SPLITT device and identified the best regimes of operating parameters. While the CE figures are found to be best represented by a group variable Π, the SI values are better represented as function of the product of the group variables γ and β; the SI versus Π plots clearly separate into two basic trends: one for constant β (i.e., varying γ) and the other for constant γ (i.e., varying β). Our study prescribes the desired operating regimes of a microfluidic magnetophoretic SPLITT device in a practical immunomagnetic separation application.     

CARMEL-2: A second generation VLSI architecture for Flat Concurrent Prolog

CARMEL-2 is a high performance VLSI uniprocessor, tuned forFlat Concurrent Prolog (FCP). CARMEL-2 shows almost 5-fold speedup over its predecessor, CARMEL-1, and it achieves 2,400 KLIPS executingappend. This high execution rate was gained as a result of an optimized design, based on an extensive architecture-oriented execution analysis of FCP, and the lessons learned with CARMEL-1. CARMEL-2 is a RISC processor in its character and performance. The instruction set includes only 29 carefully selected instructions. The 10 special instructions, the prudent implementation and pipeline scheme, as well as sophisticated mechanisms such as intelligent dereference, distinguish CARMEL-2 as a RISC processor for FCP.     

A method of DDoS attack detection using HTTP packet pattern and rule engine in cloud computing environment

Cloud computing is a more advanced technology for distributed processing, e.g., a thin client and grid computing, which is implemented by means of virtualization technology for servers and storages, and advanced network functionalities. However, this technology has certain disadvantages such as monotonous routing for attacks, easy attack method, and tools. This means that all network resources and operations are blocked all at once in the worst case. Various studies such as pattern analyses and network-based access control for infringement response based on Infrastructure as a Service, Platform as a Service and Software as a Service in cloud computing services have therefore been recently conducted. This study proposes a method of integration between HTTP GET flooding among Distributed Denial-of-Service attacks and MapReduce processing for fast attack detection in a cloud computing environment. In addition, experiments on the processing time were conducted to compare the performance with a pattern detection of the attack features using Snort detection based on HTTP packet patterns and log data from a Web server. The experimental results show that the proposed method is better than Snort detection because the processing time of the former is shorter with increasing congestion.     

Performance analysis of SSE and AVX instructions in multi-core CPUs and GPU computing on FDTD scheme for solid and fluid vibration problems

In this work a unified treatment of solid and fluid vibration problems is developed by means of the Finite-Difference Time-Domain (FDTD). The scheme here proposed takes advantage from a scaling factor in the velocity fields that improves the performance of the method and the vibration analysis in heterogenous media. Moreover, the scheme has been extended in order to simulate both the propagation in porous media and the lossy solid materials. In order to accurately reproduce the interaction of fluids and solids in FDTD both time and spatial resolutions must be reduced compared with the set up used in acoustic FDTD problems. This aspect implies the use of bigger grids and hence more time and memory resources. For reducing the time simulation costs, FDTD code has been adapted in order to exploit the resources available in modern parallel architectures. For CPUs the implicit usage of the advanced vectorial extensions (AVX) in multi-core CPUs has been considered. In addition, the computation has been distributed along the different cores available by means of OpenMP directives. Graphic Processing Units have been also considered and the degree of improvement achieved by means of this parallel architecture has been compared with the highly-tuned CPU scheme by means of the relative speed up. The speed up obtained by the parallel versions implemented were up to 3 (AVX and OpenMP) and 40 (CUDA) times faster than the best sequential version for CPU that also uses OpenMP with auto-vectorization techniques, but non includes implicitely vectorial instructions. Results obtained with both parallel approaches demonstrate that massive parallel programming techniques are mandatory in solid-vibration problems with FDTD.     

CPMD-mindful task assignment for NPS-F

The multiprocessor scheduling scheme NPS-F for sporadic tasks has a high utilisation bound and an overall number of preemptions bounded at design time. NPS-F binpacks tasks offline to as many servers as needed. At runtime, the scheduler ensures that each server is mapped to at most one of the m processors, at any instant. When scheduled, servers use EDF to select which of their tasks to run. Yet, unlike the overall number of preemptions, the migrations per se are not tightly bounded. Moreover, we cannot know a priori which task a server will be currently executing at the instant when it migrates. This uncertainty complicates the estimation of cache-related preemption and migration costs (CPMD), potentially resulting in their overestimation. Therefore, to simplify the CPMD estimation, we propose an amended bin-packing scheme for NPS-F allowing us (i) to identify at design time, which task migrates at which instant and (ii) bound a priori the number of migrating tasks, while preserving the utilisation bound of NPS-F.     

On-chip PMA labeling of foodborne pathogenic bacteria for viable qPCR and qLAMP detection

Propidium monoazide (PMA) is a membrane impermeable molecule that covalently bonds to double stranded DNA when exposed to light and inhibits the polymerase activity, thus enabling DNA amplification detection protocols that discriminate between viable and non-viable entities. Here, we present a microfluidic device for inexpensive, fast, and simple PMA labeling for viable qPCR and qLAMP assays. The three labeling stages of mixing, incubation, and cross-linking are completed within a microfluidic device that is designed with Tesla structures for passive microfluidic mixing, bubble trappers to improve flow uniformity, and a blue LED to cross-link the molecules. Our results show that the on-chip PMA labeling is equivalent to the standard manual protocols and prevents the replication of DNA from non-viable cells in amplification assays. However, the on-chip process is faster and simpler (30 min of hands-off work), has a reduced likelihood of false negatives, and it is less expensive because it only uses 1/20th of the reagents normally consumed in standard bench protocols. We used our microfluidic device to perform viable qPCR and qLAMP for the detection of S. typhi and E. coli O157. With this device, we are able to specifically detect viable bacteria, with a limit of detection of 7.6 × 10³ and 1.1 × 10³ CFU/mL for S. typhi and E. coli O157, respectively, while eliminating amplification from non-viable cells. Furthermore, we studied the effects of greater flow rates to expedite the labeling process and identified a maximum flow rate of 0.7 μL/min for complete labeling with the current design.     

Droplet microfluidic preparation of au nanoparticles-coated chitosan microbeads for flow-through surface-enhanced Raman scattering detection

An integrated microfluidic device was fabricated to enable on-chip droplet forming, trapping, fusing, shrinking, reaction and producing functional microbeads for a flow-through single bead-based molecule detection. Dielectrophoresis (DEP) force was used to transport target polymer droplets into different predefined microwells, where the droplets were fused through electrocoalescence to form a new one with a desired diameter. In a continuous water loss process with water diffusion to oil phase, the polymer droplet was shrunken and solidified to form a polymer microbead. For a demonstration, Au nanoparticles-coated chitosan microbeads were in situ fabricated through droplet trapping, fusion and shrinking, followed by synthesis of Au nanoparticles on the microbead surface via a photoreduction process. The produced Au nanoparticle/chitosan microbead embedded in the microwell resulted in a highly sensitive, flow-through surface-enhanced Raman scattering (SERS) detection of Rhodamine 6G (R6G). This work successfully demonstrates an integrated droplet based lab-on-a chip and its application to fabricate an extremely high-throughput single bead based detection platform.     

DNA codes for nonadditive stem similarity

DNA sequences are sequences with elements from the quaternary DNA alphabet {A, C, G, T}. An important property of them is their directedness and ability to form duplexes as a result of hybridization process, i.e., coalescing two oppositely directed sequences. In biological experiments exploiting this property it is necessary to generate an ensemble of such sequences (DNA codes) consisting of pairs of DNA sequences referred to as Watson-Crick duplexes. Furthermore, for any two words of the DNA code that do not form a Watson-Crick duplex, hybridization energy—stability measure of a potential DNA duplex—is upper bounded by a constant specified by conditions of an experiment. This problem can naturally be interpreted in terms of coding theory. Continuing our previous works, we consider a nonadditive similarity function for two DNA sequences, which most adequately models their hybridization energy. For the maximum cardinality of DNA codes based on this similarity, we establish a Singleton upper bound and present an example of an optimal construction. Using ensembles of DNA codes with special constraints on codewords, which we call Fibonacci ensembles, we obtain a random-coding lower bound on the maximum cardinality of DNA codes under this similarity function.     

Parallelizing Complex Streaming Applications on Distributed Scratchpad Memory Multicore Architecture

Multicore processors can provide sufficient computing power and flexibility for complex streaming applications, such as high-definition video processing. For less hardware complexity and power consumption, the distributed scratchpad memory architecture is considered, instead of the cache memory architecture. However, the distributed design poses new challenges to programming. It is difficult to exploit all available capabilities and achieve maximal throughput, due to the combined complexity of inter-processor communication, synchronization, and workload balancing. In this study, we developed an efficient design flow for parallelizing multimedia applications on a distributed scratchpad memory multicore architecture. An application is first partitioned into streaming components and then mapped onto multicore processors. Various hardware-dependent factors and application-specific characteristics are involved in generating efficient task partitions and allocating resources appropriately. To test and verify the proposed design flow, three popular multimedia applications were implemented: a full-HD motion JPEG decoder, an object detector, and a full-HD H.264/AVC decoder. For demonstration purposes, SONY PlayStation \(^{\circledR }\) 3 was selected as the target platform. Simulation results show that, on PS3, the full-HD motion JPEG decoder with the proposed design flow can decode about 108.9 frames per second (fps) in the 1080p format. The object detection application can perform real-time object detection at 2.84 fps at \(1280 \times 960\) resolution, 11.75 fps at \(640 \times 480\) resolution, and 62.52 fps at \(320 \times 240\) resolution. The full-HD H.264/AVC decoder applications can achieve nearly 50 fps.     

Stack method in program semantics

In this paper,we describe firstly a formal concept of stack and introduce some operational rules on it.Then we extend the denotational semantics to“the denotational semantics with stacks”,by which we makea formal semantics for a real PASCAL(subset)which can run on a computer.By an example of programwith procedures it will be seen that our method can be used to describe the basic principles of compiling.Finally,we have succeeded in building a formal semantics model of a PROLOG(subset).     

JackHare: a framework for SQL to NoSQL translation using MapReduce

As data exploration has increased rapidly in recent years, the datastore and data processing are getting more and more attention in extracting important information. To find a scalable solution to process the large-scale data is a critical issue in either the relational database system or the emerging NoSQL database. With the inherent scalability and fault tolerance of Hadoop, MapReduce is attractive to process the massive data in parallel. Most of previous researches focus on developing the SQL or SQL-like queries translator with the Hadoop distributed file system. However, it could be difficult to update data frequently in such file system. Therefore, we need a flexible datastore as HBase not only to place the data over a scale-out storage system, but also to manipulate the changeable data in a transparent way. However, the HBase interface is not friendly enough for most users. A GUI composed of SQL client application and database connection to HBase will ease the learning curve. In this paper, we propose the JackHare framework with SQL query compiler, JDBC driver and a systematical method using MapReduce framework for processing the unstructured data in HBase. After importing the JDBC driver to a SQL client GUI, we can exploit the HBase as the underlying datastore to execute the ANSI-SQL queries. Experimental results show that our approaches can perform well with efficiency and scalability.     

Adaptive AMG with coarsening based on compatible weighted matching

We introduce a new composite adaptive Algebraic Multigrid (composite \(\alpha \) AMG) method to solve systems of linear equations without a-priori knowledge or assumption on characteristics of near-null components of the AMG preconditioned problem referred to as algebraic smoothness. Our version of \(\alpha \) AMG is a composite solver built through a bootstrap strategy aimed to obtain a desired convergence rate. The coarsening process employed to build each new solver component relies on a pairwise aggregation scheme based on weighted matching in a graph, successfully exploited for reordering algorithms in sparse direct methods to enhance diagonal dominance, and compatible relaxation. The proposed compatible matching process replaces the commonly used characterization of strength of connection in both the coarse space selection and in the interpolation scheme. The goal is to design a method leading to scalable AMG for a wide class of problems that go beyond the standard elliptic Partial Differential Equations (PDEs). In the present work, we introduce the method and demonstrate its potential when applied to symmetric positive definite linear systems arising from finite element discretization of highly anisotropic elliptic PDEs on structured and unstructured meshes. We also report on some preliminary tests for 2D and 3D elasticity problems as well as on problems from the University of Florida Sparse Matrix Collection.