bluuebunny/crossref_metadata_2025 huggingface dataset:
VMScatter
Authors: Cui Lei , Li Jianxin , Li Bo , Huai Jinpeng , Hu Chunming , Wo Tianyu , Al-Aqrabi Hussain , Liu Lu
Published: August 2013

Live virtual machine migration is a technique often used to migrate an entire OS with running applications in a non-disruptive fashion. Prior works concerned with one-to-one live migration with many techniques have been proposed such as pre-copy, post-copy and log/replay. In contrast, we propose VMScatter, a one-to-many migration method to migrate virtual machines from one to many other hosts simultaneously. First, by merging the identical pages within or across virtual machines, VMScatter multicasts only a single copy of these pages to associated target hosts for avoiding redundant transmission. This is impactful practically when the same OS and similar applications running in the virtual machines where there are plenty of identical pages. Second, we introduce a novel grouping algorithm to decide the placement of virtual machines, distinguished from the previous schedule algorithms which focus on the workload for load balance or power saving, we also focus on network traffic, which is a critical metric in data-intensive data centers. Third, we schedule the multicast sequence of packets to reduce the network overhead introduced by joining or quitting the multicast groups of target hosts. Compared to traditional live migration technique in QEMU/KVM, VMScatter reduces 74.2% of the total transferred data, 69.1% of the total migration time and achieves the network traffic reduction from 50.1% to 70.3%.
A lightweight VMM on many core for high performance computing
Authors: Dai Yuehua , Qi Yong , Ren Jianbao , Shi Yi , Wang Xiaoguang , Yu Xuan
Published: August 2013

Traditional Virtual Machine Monitor (VMM) virtualizes some devices and instructions, which induces performance overhead to guest operating systems. Furthermore, the virtualization contributes a large amount of codes to VMM, which makes a VMM prone to bugs and vulnerabilities.

On the other hand, in cloud computing, cloud service provider configures virtual machines based on requirements which are specified by customers in advance. As resources in a multi-core server increase to more than adequate in the future, virtualization is not necessary although it provides convenience for cloud computing. Based on the above observations, this paper presents an alternative way for constructing a VMM: configuring a booting interface instead of virtualization technology. A lightweight virtual machine monitor - OSV is proposed based on this idea. OSV can host multiple full functional Linux kernels with little performance overhead. There are only 6 hyper-calls in OSV. The Linux running on top of OSV is intercepted only for the inter-processor interrupts. The resource isolation is implemented with hardware-assist virtualization. The resource sharing is controlled by distributed protocols embedded in current operating systems.

We implement a prototype of OSV on AMD Opteron processor based 32-core servers with SVM and cache-coherent NUMA architectures. OSV can host up to 8 Linux kernels on the server with less than 10 lines of code modifications to Linux kernel. OSV has about 8000 lines of code which can be easily tuned and debugged. The experiment results show that OSV VMM has 23.7% performance improvement compared with Xen VMM.
Leveraging phase change memory to achieve efficient virtual machine execution
Authors: Zhou Ruijin , Li Tao
Published: August 2013

Virtualization technology is being widely adopted by servers and data centers in the cloud computing era to improve resource utilization and energy efficiency. Nevertheless, the heterogeneous memory demands from multiple virtual machines (VM) make it more challenging to design efficient memory systems. Even worse, mission critical VM management activities (e.g. checkpointing) could incur significant runtime overhead due to intensive IO operations. In this paper, we propose to leverage the adaptable and non-volatile features of the emerging phase change memory (PCM) to achieve efficient virtual machine execution. Towards this end, we exploit VM-aware PCM management mechanisms, which 1) smartly tune SLC/MLC page allocation within a single VM and across different VMs and 2) keep critical checkpointing pages in PCM to reduce I/O traffic. Experimental results show that our single VM design (IntraVM) improves performance by 10% and 20% compared to pure SLC- and MLC- based systems. Further incorporating VM-aware resource management schemes (IntraVM+InterVM) increases system performance by 15%. In addition, our design saves 46% of checkpoint/restore duration and reduces 50% of overall IO penalty to the system.
Data-only flattening for nested data parallelism
Authors: Bergstrom Lars , Fluet Matthew , Rainey Mike , Reppy John , Rosen Stephen , Shaw Adam
Published: August 2013

Data parallelism has proven to be an effective technique for high-level programming of a certain class of parallel applications, but it is not well suited to irregular parallel computations. Blelloch and others proposed
nested data parallelism
(NDP) as a language mechanism for programming irregular parallel applications in a declarative data-parallel style. The key to this approach is a compiler transformation that flattens the NDP computation and data structures into a form that can be executed efficiently on a wide-vector SIMD architecture. Unfortunately, this technique is ill suited to execution on today's multicore machines. We present a new technique, called
data-only flattening
, for the compilation of NDP, which is suitable for multicore architectures. Data-only flattening transforms nested data structures in order to expose programs to various optimizations while leaving control structures intact. We present a formal semantics of data-only flattening in a core language with a rewriting system. We demonstrate the effectiveness of this technique in the Parallel ML implementation and we report encouraging experimental results across various benchmark applications.
FastLane
Authors: Wamhoff Jons-Tobias , Fetzer Christof , Felber Pascal , Rivière Etienne , Muller Gilles
Published: August 2013

Software transactional memory (STM) can lead to scalable implementations of concurrent programs, as the
relative
performance of an application increases with the number of threads that support it. However, the
absolute
performance is typically impaired by the overheads of transaction management and instrumented accesses to shared memory. This often leads STM-based programs with low thread counts to perform worse than a sequential, non-instrumented version of the same application.

In this paper, we propose FastLane, a new STM algorithm that bridges the performance gap between sequential execution and classical STM algorithms when running on few cores. FastLane seeks to reduce instrumentation costs and thus performance degradation in its target operation range. We introduce a novel algorithm that differentiates between two types of threads: One thread (the master) executes transactions pessimistically without ever aborting, thus with minimal instrumentation and management costs, while other threads (the helpers) can commit speculative transactions only when they do not conflict with the master. Helpers thus contribute to the application progress without impairing on the performance of the master.

We implement FastLane as an extension of a state-of-the-art STM runtime system and compiler. Multiple code paths are produced for execution on a single, few, and many cores. The runtime system selects the code path providing the best throughput, depending on the number of cores available on the target machine. Evaluation results indicate that our approach provides promising performance at low thread counts: FastLane almost systematically wins over a classical STM in the 1-6 threads range, and often performs better than sequential execution of the non-instrumented version of the same application starting with 2 threads.
From relational verification to SIMD loop synthesis
Authors: Barthe Gilles , Crespo Juan Manuel , Gulwani Sumit , Kunz Cesar , Marron Mark
Published: August 2013

Existing pattern-based compiler technology is unable to effectively exploit the full potential of SIMD architectures. We present a new program synthesis based technique for auto-vectorizing performance critical innermost loops. Our synthesis technique is applicable to a wide range of loops, consistently produces performant SIMD code, and generates correctness proofs for the output code. The synthesis technique, which leverages existing work on relational verification methods, is a novel combination of deductive loop restructuring, synthesis condition generation and a new inductive synthesis algorithm for producing loop-free code fragments. The inductive synthesis algorithm wraps an optimized depth-first exploration of code sequences inside a CEGIS loop. Our technique is able to quickly produce SIMD implementations (up to 9 instructions in 0.12 seconds) for a wide range of fundamental looping structures. The resulting SIMD implementations outperform the original loops by 2.0x-3.7x.
Morph algorithms on GPUs
Authors: Nasre Rupesh , Burtscher Martin , Pingali Keshav
Published: August 2013

There is growing interest in using GPUs to accelerate graph algorithms such as breadth-first search, computing page-ranks, and finding shortest paths. However, these algorithms do not modify the graph structure, so their implementation is relatively easy compared to general graph algorithms like mesh generation and refinement, which
morph
the underlying graph in non-trivial ways by adding and removing nodes and edges. We know relatively little about how to implement morph algorithms efficiently on GPUs.

In this paper, we present and study four morph algorithms: (i) a computational geometry algorithm called Delaunay Mesh Refinement (DMR), (ii) an approximate SAT solver called Survey Propagation (SP), (iii) a compiler analysis called Points-To Analysis (PTA), and (iv) Boruvka's Minimum Spanning Tree algorithm (MST). Each of these algorithms modifies the graph data structure in different ways and thus poses interesting challenges.

We overcome these challenges using algorithmic and GPU-specific optimizations. We propose efficient techniques to perform concurrent subgraph addition, subgraph deletion, conflict detection and several optimizations to improve the scalability of morph algorithms. For an input mesh with 10 million triangles, our DMR code achieves an 80x speedup over the highly optimized serial
Triangle
program and a 2.3x speedup over a multicore implementation running with 48 threads. Our SP code is 3x faster than a multicore implementation with 48 threads on an input with 1 million literals. The PTA implementation is able to analyze six SPEC 2000 benchmark programs in just 74 milliseconds, achieving a geometric mean speedup of 9.3x over a 48-thread multicore version. Our MST code is slower than a multicore version with 48 threads for sparse graphs but significantly faster for denser graphs.

This work provides several insights into how other morph algorithms can be efficiently implemented on GPUs.
NUMA-aware reader-writer locks
Authors: Calciu Irina , Dice Dave , Lev Yossi , Luchangco Victor , Marathe Virendra J. , Shavit Nir
Published: August 2013

Non-Uniform Memory Access (NUMA) architectures are gaining importance in mainstream computing systems due to the rapid growth of multi-core multi-chip machines. Extracting the best possible performance from these new machines will require us to revisit the design of the concurrent algorithms and synchronization primitives which form the building blocks of many of today's applications. This paper revisits one such critical synchronization primitive -- the reader-writer lock.

We present what is, to the best of our knowledge, the first family of reader-writer lock algorithms tailored to NUMA architectures. We present several variations which trade fairness between readers and writers for higher concurrency among readers and better back-to-back batching of writers from the same NUMA node. Our algorithms leverage the
lock cohorting
technique to manage synchronization between writers in a NUMA-friendly fashion, binary flags to coordinate readers and writers, and simple distributed reader counter implementations to enable NUMA-friendly concurrency among readers. The end result is a collection of surprisingly simple NUMA-aware algorithms that outperform the state-of-the-art reader-writer locks by up to a factor of 10 in our microbenchmark experiments. To evaluate our algorithms in a realistic setting we also present performance results of the kccachetest benchmark of the
Kyoto-Cabinet
distribution, an open-source database which makes heavy use of pthread reader-writer locks. Our locks boost the performance of kccachetest by up to 40% over the best prior alternatives.
Parallel suffix array and least common prefix for the GPU
Authors: Deo Mrinal , Keely Sean
Published: August 2013

Suffix Array (SA) is a data structure formed by sorting the suffixes of a string into lexicographic order. SAs have been used in a variety of applications, most notably in pattern matching and Burrows-Wheeler Transform (BWT) based lossless data compression. SAs have also become the data structure of choice for many, if not all, string processing problems to which suffix tree methodology is applicable. Over the last two decades researchers have proposed many suffix array construction algorithm (SACAs). We do a systematic study of the main classes of SACAs with the intent of mapping them onto a data parallel architecture like the GPU. We conclude that
skew algorithm
[12], a linear time recursive algorithm, is the best candidate for GPUs as all its phases can be efficiently mapped to a data parallel hardware. Our OpenCL implementation of
skew algorithm
achieves a throughput of up to 25 MStrings/sec and a speedup of up to 34x and 5.8x over a single threaded CPU implementation using a discrete GPU and APU respectively. We also compare our OpenCL implementation against the fastest known CPU implementation based on
induced copying
and achieve a speedup of up to 3.7x. Using SA we construct BWT on GPU and achieve a speedup of 11x over the fastest known BWT on GPU.

Suffix arrays are often augmented with the longest common prefix (LCP) information. We design a novel high-performance parallel algorithm for computing LCP on the GPU. Our GPU implementation of LCP achieves a speedup of up to 25x and 4.3x on discrete GPU and APU respectively.
Scalable deterministic replay in a parallel full-system emulator
Authors: Chen Yufei , Chen Haibo
Published: August 2013

Full-system emulation has been an extremely useful tool in developing and debugging systems software like operating systems and hypervisors. However, current full-system emulators lack the support for deterministic replay, which limits the reproducibility of concurrency bugs that is indispensable for analyzing and debugging the essentially multi-threaded systems software.

This paper analyzes the challenges in supporting deterministic replay in parallel full-system emulators and makes a comprehensive study on the sources of non-determinism. Unlike application-level replay systems, our system, called ReEmu, needs to log sources of non-determinism in both the guest software stack and the dynamic binary translator for faithful replay. To provide scalable and efficient record and replay on multicore machines, ReEmu makes several notable refinements to the CREW protocol that replays shared memory systems. First, being aware of the performance bottlenecks in frequent lock operations in the CREW protocol, ReEmu refines the CREW protocol with a seqlock-like design, to avoid serious contention and possible starvation in instrumentation code tracking dependence of racy accesses on a shared memory object. Second, to minimize the required log files, ReEmu only logs minimal local information regarding accesses to a shared memory location, but instead relies on an offline log processing tool to derive precise shared memory dependence for faithful replay. Third, ReEmu adopts an automatic lock clustering mechanism that clusters a set of uncontended memory objects to a bulk to reduce the frequencies of lock operations, which noticeably boost performance.

Our prototype ReEmu is based on our open-source COREMU system and supports scalable and efficient record and replay of full-system environments (both x64 and ARM). Performance evaluation shows that ReEmu has very good performance scalability on an Intel multicore machine. It incurs only 68.9% performance overhead on average (ranging from 51.8% to 94.7%) over vanilla COREMU to record five PARSEC benchmarks running on a 16-core emulated system.
StreamScan
Authors: Yan Shengen , Long Guoping , Zhang Yunquan
Published: August 2013

Scan (also known as prefix sum) is a very useful primitive for various important parallel algorithms, such as sort, BFS, SpMV, compaction and so on. Current state of the art of GPU based scan implementation consists of three consecutive Reduce-Scan-Scan phases. This approach requires at least two global barriers and 3N (N is the problem size) global memory accesses. In this paper we propose StreamScan, a novel approach to implement scan on GPUs with only one computation phase. The main idea is to restrict synchronization to only adjacent workgroups, and thereby eliminating global barrier synchronization completely. The new approach requires only 2N global memory accesses and just one kernel invocation. On top of this we propose two important op-timizations to further boost performance speedups, namely thread grouping to eliminate unnecessary local barriers, and register optimization to expand the on chip problem size. We designed an auto-tuning framework to search the parameter space automatically to generate highly optimized codes for both AMD and Nvidia GPUs. We implemented our technique with OpenCL. Compared with previous fast scan implementations, experimental results not only show promising performance speedups, but also reveal dramatic different optimization tradeoffs between Nvidia and AMD GPU platforms.
Using hardware transactional memory to correct and simplify and readers-writer lock algorithm
Authors: Dice Dave , Lev Yossi , Liu Yujie , Luchangco Victor , Moir Mark
Published: August 2013

Designing correct synchronization algorithms is notoriously difficult, as evidenced by a bug we have identified that has apparently gone unnoticed in a well-known synchronization algorithm for nearly two decades. We use hardware transactional memory (HTM) to construct a corrected version of the algorithm. This version is significantly simpler than the original and furthermore improves on it by eliminating usage constraints and reducing space requirements. Performance of the HTM-based algorithm is competitive with the original in "normal" conditions, but it does suffer somewhat under heavy contention. We successfully apply some optimizations to help close this gap, but we also find that they are incompatible with known techniques for improving progress properties. We discuss ways in which future HTM implementations may address these issues. Finally, although our focus is on how effectively HTM can correct and simplify the algorithm, we also suggest bug fixes and workarounds that do not depend on HTM.
Automatic problem size sensitive task partitioning on heterogeneous parallel systems
Authors: Grasso Ivan , Kofler Klaus , Cosenza Biagio , Fahringer Thomas
Published: August 2013

In this paper we propose a novel approach which automatizes task partitioning in heterogeneous systems. Our framework is based on the Insieme Compiler and Runtime infrastructure. The compiler translates a single-device OpenCL program into a multi-device OpenCL program. The runtime system then performs dynamic task partitioning based on an offline-generated prediction model. In order to derive the prediction model, we use a machine learning approach that incorporates static program features as well as dynamic, input sensitive features. Our approach has been evaluated over a suite of 23 programs and achieves performance improvements compared to an execution of the benchmarks on a single CPU and a single GPU only.
Decomposition techniques for optimal design-space exploration of streaming applications
Authors: Padmanabhan Shobana , Chen Yixin , Chamberlain Roger D.
Published: August 2013

Streaming data programs are an important class of applications, for which queueing network models are frequently available. While the design space can be large, decomposition techniques can be effective at design space reduction. We introduce two decomposition techniques called convex decomposition and unchaining and present implications for a biosequence search application.
Expressing graph algorithms using generalized active messages
Authors: Edmonds Nick , Willcock Jeremiah , Lumsdaine Andrew
Published: August 2013

Recently, graph computation has emerged as an important class of high-performance computing application whose characteristics differ markedly from those of traditional, compute-bound, kernels. Libraries such as BLAS, LAPACK, and others have been successful in codifying best practices in numerical computing. The data-driven nature of graph applications necessitates a more complex application stack incorporating runtime optimization. In this paper, we present a method of phrasing graph algorithms as collections of asynchronous, concurrently executing, concise code fragments which may be invoked both locally and in remote address spaces. A runtime layer performs a number of dynamic optimizations, including message coalescing, message combining, and software routing. Practical implementations and performance results are provided for a number of representative algorithms.
Multi-level parallel computing of reverse time migration for seismic imaging on blue Gene/Q
Authors: Lu Ligang , Magerlein Karen
Published: August 2013

Blue Gene/Q (BG/Q) is an early representative of increasing scale and thread count that will characterize future HPC systems: large counts of nodes, cores, and threads; and a rich programming environment with many degrees of freedom in parallel computing optimization. So it is both a challenge and an opportunity to it to accelerate the seismic imaging applications to the unprecedented levels that will significantly advance the technologies for the oil and gas industry. In this work we aim to address two important questions: how HPC systems with high levels of scale and thread count will perform in real applications; and how systems with many degrees of freedom in parallel programming can be calibrated to achieve optimal performance. Based on BG/Q's architecture features and RTM workload characteristics, we developed massive domain partition, MPI , and SIMD Our detailed deep analyses in various aspects of optimization also provide valuable experience and insights into how can be utilized to facilitate the advance of seismic imaging technologies. Our BG/Q RTM solution achieved a 14.93x speedup over the BG/P implementation. Our multi-level parallelism strategies for Reverse Time Migration (RTM) seismic imaging computing on BG/Q provides an example of how HPC systems like BG/Q can accelerate applications to a new level.
On the Domination Polynomial of Some Graph Operations
Authors: Alikhani Saeid
Published: August 2013

Let G be a simple graph of order n. The domination polynomial of G is the polynomial D(G,λ)=∑i=0n‍d(G,i)λi, where d(G,i) is the number of dominating sets of G of size i. Every root of D(G,λ) is called the domination root of G. In this paper, we study the domination polynomial of some graph operations.
Scan and Paint: Theory and Practice of a Sound Field Visualization Method
Authors: Comesaña Daniel Fernández , Steltenpool Steven , Carrillo Pousa Graciano , de Bree Hans-Elias , Holland Keith R.
Published: August 2013

Sound visualization techniques have played a key role in the development of acoustics throughout history. The development of measurement apparatus and techniques for displaying sound and vibration phenomena has provided excellent tools for building understanding about specific problems. Traditional methods, such as step-by-step measurements or simultaneous multichannel systems, have a strong tradeoff between time requirements, flexibility, and cost. However, if the sound field can be assumed time stationary, scanning methods allow us to assess variations across space with a single transducer, as long as the position of the sensor is known. The proposed technique, Scan and Paint, is based on the acquisition of sound pressure and particle velocity by manually moving a P-U probe (pressure-particle velocity sensors) across a sound field whilst filming the event with a camera. The sensor position is extracted by applying automatic color tracking to each frame of the recorded video. It is then possible to visualize sound variations across the space in terms of sound pressure, particle velocity, or acoustic intensity. In this paper, not only the theoretical foundations of the method, but also its practical applications are explored such as scanning transfer path analysis, source radiation characterization, operational deflection shapes, virtual phased arrays, material characterization, and acoustic intensity vector field mapping.
Rheological and Mechanical Characterization of Renewable Resource Based High Molecular Weight PLA Nanocomposites
Authors: Jandas P. J. , Mohanty S. , Nayak S. K.
Published: August 2013

The present study discusses structural aspects of nanocomposites and the ability of layered nanosilicates to alter the flow behaviour of poly(lactic acid) (PLA) melts. In addition, dynamic and static mechanical properties of PLA nanocomposites prepared from melt mixing method have been also discussed. A comparative study of nanocomposite properties has been conducted using two different nanoclays, natural montmorillonite modified with alkyl ammonium surfactant (OMMT), and commercially available organosilicate, Cloisite 30B, as reinforcements within the PLA matrix. Since OMMT has undergone better intercalation within the matrix, the corresponding nanocomposite showed superior mechanical and rheological characteristics than its C30B counterpart.
Arc Length Inequality for a Certain Class of Analytic Functions Related to Conic Regions
Authors: Ul-Haq Wasim , Arif Muhammad , Khan Asfandyar
Published: August 2013

In our present investigation, we
introduce a subclass of analytic function associated with conic regions
which is a form of generalized close-to-convexity. The arc-length inequality
for a class of analytic function is well known. We derive this inequality
for the newly defined class and also study some of its interesting
consequences.
Antimicrobial Ionic Liquids with Fumarate Anion
Authors: He Biyan , Ou Guangnan , Zhou Changyi , Wang Meihong , Chen Suyan
Published: August 2013

The shortage of new antimicrobial drugs and increasing resistance of microbe to antimicrobial agents have been of some concern. The formulation studies of new antibacterial and antifungal agents have been an active research field. Ionic liquids are known as designed liquids with controllable physical/chemical/biological properties and specific functions, which have been attracting considerable interest over recent years. However, no attention has been made towards the preparation of ionic liquids with antimicrobial activities. In this paper, a new class of ionic liquids (ILs) with fumarate anion was synthesized by neutralization of aqueous 1‐butyl‐3‐methylimidazolium hydroxide with equimolar monoester fumarate and characterized using NMR and thermal gravimetric analysis. The ILs are soluble in water and polar organic solvents and also soluble in the common ILs. The antimicrobial activities of the ILs are more active than commercially available potassium sorbate and are greatly affected by the alkyl chain length. The significant antimicrobial properties observed in this research suggest that the ILs may have potential applications in the modern biotechnology.
A New Coated Nitinol Occluder for Transcatheter Closure of Ventricular Septal Defects in a Canine Model
Authors: Zhou Yong , Chen Feng , Huang Xinmiao , Zhao Xianxian , Wu Hong , Bai Yuan , Qin Yongwen
Published: August 2013

Aims. This study evaluated feasibility and safety of implanting the polyester-coated nitinol ventricular septal defect occluder (pcVSDO) in the canine model.Methods and Results. VSD models were successfully established by transseptal ventricular septal puncture via the right jugular vein in 15 out of 18 canines. Two types of VSDOs were implanted, either with pcVSDOs (n=8) as the new type occluder group or with the commercial ventricular septal defect occluders (VSDOs,n=7, Shanghai Sharp Memory Alloy Co. Ltd.) as the control group. Sheath size was 10 French (10 Fr) in two groups. Then the general state of the canines was observed after implantation. ECG and TTE were performed, respectively, at 7, 30, 90 days of follow-up. The canines were sacrificed at these time points for pathological and scanning electron microscopy examination. The devices were successfully implanted in all 15 canines and were retrievable and repositionable. There was no thrombus formation on the device or occurrence of complete heart block. The pcVSDO surface implanted at day 7 was already covered with neotissue by gross examination, and it completed endothelialization at day 30, while the commercial VSDO was covered with the neotissue in 30th day and the complete endothelialization in 90th day.Conclusion. The study shows that pcVSDO is feasible and safe to close canine VSD model and has good biocompatibility and shorter time of endothelialization.
Thermophysical Properties of Binary Liquid Systems of Ethanoic Acid, Propanoic Acid, and Butanoic Acid with Benzene or Acetophenone
Authors: Ahluwalia R. , Gupta Ritu , Vashisht J. L. , Wanchoo R. K.
Published: August 2013

The density (), viscosity (), and surface tension () of binary mixtures of carboxylic acids (CAs) (ethanoic acid (EA), propanoic acid (PA), butanoic acid (BA)) + benzene (BEN) or acetophenone (ACT) have been measured at 298.15, 308.15, and 318.15 K. From the experimental results, excess values of molar volume (), viscosity (), Gibb's free energy for the activation of low (), and surface tension () were evaluated and fitted to a Redlich-Kister type of equation. The parameter “” of Grunberg and Nissan expression has also been calculated. From the sign and magnitude of , , , , and “” values, it is concluded that specific interactions are present in CA+ACT system and these interactions are absent in CA + BEN mixtures. Various viscosity and surface tension models have been used to test the consistency of the data.
A Review on the Use of Grid-Based Boltzmann Equation Solvers for Dose Calculation in External Photon Beam Treatment Planning
Authors: Kan Monica W. K. , Yu Peter K. N. , Leung Lucullus H. T.
Published: August 2013

Deterministic linear Boltzmann transport equation (D-LBTE) solvers have recently been developed, and one of the latest available software codes, Acuros XB, has been implemented in a commercial treatment planning system for radiotherapy photon beam dose calculation. One of the major limitations of most commercially available model-based algorithms for photon dose calculation is the ability to account for the effect of electron transport. This induces some errors in patient dose calculations, especially near heterogeneous interfaces between low and high density media such as tissue/lung interfaces. D-LBTE solvers have a high potential of producing accurate dose distributions in and near heterogeneous media in the human body. Extensive previous investigations have proved that D-LBTE solvers were able to produce comparable dose calculation accuracy as Monte Carlo methods with a reasonable speed good enough for clinical use. The current paper reviews the dosimetric evaluations of D-LBTE solvers for external beam photon radiotherapy. This content summarizes and discusses dosimetric validations for D-LBTE solvers in both homogeneous and heterogeneous media under different circumstances and also the clinical impact on various diseases due to the conversion of dose calculation from a conventional convolution/superposition algorithm to a recently released D-LBTE solver.
Cryobiopsy: Should This Be Used in Place of Endobronchial Forceps Biopsies?
Authors: Rubio Edmundo R. , le Susanti R. , Whatley Ralph E. , Boyd Michael B.
Published: August 2013

Forceps biopsies of airway lesions have variable yields. The yield increases when combining techniques in order to collect more material. With the use of cryotherapy probes (cryobiopsy) larger specimens can be obtained, resulting in an increase in the diagnostic yield. However, the utility and safety of cryobiopsy with all types of lesions, including flat mucosal lesions, is not established.Aims. Demonstrate the utility/safety of cryobiopsy versus forceps biopsy to sample exophytic and flat airway lesions.Settings and Design. Teaching hospital-based retrospective analysis.Methods. Retrospective analysis of patients undergoing cryobiopsies (singly or combined with forceps biopsies) from August 2008 through August 2010.Statistical Analysis. Wilcoxon signed-rank test.Results. The comparative analysis of 22 patients with cryobiopsy and forceps biopsy of the same lesion showed the mean volumes of material obtained with cryobiopsy were significantly larger (0.696 cm3versus 0.0373 cm3,P=0.0014). Of 31 cryobiopsies performed, one had minor bleeding. Cryopbiopsy allowed sampling of exophytic and flat lesions that were located centrally or distally. Cryobiopsies were shown to be safe, free of artifact, and provided a diagnostic yield of 96.77%.Conclusions. Cryobiopsy allows safe sampling of exophytic and flat airway lesions, with larger specimens, excellent tissue preservation and high diagnostic accuracy.
Magnesium Coated Bioresorbable Phosphate Glass Fibres: Investigation of the Interface between Fibre and Polyester Matrices
Authors: Liu Xiaoling , Grant David M. , Parsons Andrew J. , Harper Lee T. , Rudd Chris D. , Ahmed Ifty
Published: August 2013

Bioresorbable phosphate glass fibre reinforced polyester composites have been investigated as replacement for some traditional metallic orthopaedic implants, such as bone fracture fixation plates. However, composites tested revealed loss of the interfacial integrity after immersion within aqueous media which resulted in rapid loss of mechanical properties. Physical modification of fibres to change fibre surface morphology has been shown to be an effective method to improve fibre and matrix adhesion in composites. In this study, biodegradable magnesium which would gradually degrade to Mg2+in the human body was deposited via magnetron sputtering onto bioresorbable phosphate glass fibres to obtain roughened fibre surfaces. Fibre surface morphology after coating was observed using scanning electron microscope (SEM). The roughness profile and crystalline texture of the coatings were determined via atomic force microscope (AFM) and X-ray diffraction (XRD) analysis, respectively. The roughness of the coatings was seen to increase from40±1 nm to80±1 nm. The mechanical properties (tensile strength and modulus) of fibre with coatings decreased with increased magnesium coating thickness.
Auditory Verbal Cues Alter the Perceived Flavor of Beverages and Ease of Swallowing: A Psychometric and Electrophysiological Analysis
Authors: Nakamura Aya , Imaizumi Satoshi
Published: August 2013

We investigated the possible effects of auditory verbal cues on flavor perception and swallow physiology for younger and elder participants. Apple juice, aojiru (grass) juice, and water were ingested with or without auditory verbal cues. Flavor perception and ease of swallowing were measured using a visual analog scale and swallow physiology by surface electromyography and cervical auscultation. The auditory verbal cues had significant positive effects on flavor and ease of swallowing as well as on swallow physiology. The taste score and the ease of swallowing score significantly increased when the participant’s anticipation was primed by accurate auditory verbal cues. There was no significant effect of auditory verbal cues on distaste score. Regardless of age, the maximum suprahyoid muscle activity significantly decreased when a beverage was ingested without auditory verbal cues. The interval between the onset of swallowing sounds and the peak timing point of the infrahyoid muscle activity significantly shortened when the anticipation induced by the cue was contradicted in the elderly participant group. These results suggest that auditory verbal cues can improve the perceived flavor of beverages and swallow physiology.
Combined Treatment of Hydroxytyrosol with Carbon Monoxide-Releasing Molecule-2 Prevents TNFα-Induced Vascular Endothelial Cell Dysfunction through NO Production with Subsequent NFκB Inactivation
Authors: Zrelli Houda , Wei Wu Che , Zghonda Nahla , Shimizu Hidehisa , Miyazaki Hitoshi
Published: August 2013

This study investigated the atheroprotective properties of olive oil polyphenol, hydroxytyrosol (HT), in combination with carbon monoxide-releasing molecule-2 (CORM-2) that acts as a carbon monoxide donor using vascular endothelial cells (VECs). Our results showed that CORM-2 could strengthen the cytoprotective and anti-apoptotic effects of HT against TNFα-induced cellular damage by enhancing cell survival and the suppression of caspase-3 activation. While HT alone attenuated NFκBp65 phosphorylation and IκBαdegradation triggered by TNFαin a dose-dependent manner, combined treatment of HT with CORM-2 but not iCORM-2 nearly completely blocked these TNFαeffects. Furthermore, combined action of both compounds results in the inhibition of NFκB nuclear translocation. Results also indicate that both compounds time-dependently increased eNOS phosphorylation levels and the combination of HT with CORM-2 was more effective in enhancing eNOS activation and NO production in VECs. The NOS inhibitor, L-NMMA, significantly suppressed the combined effects of HT and CORM-2 on TNFα-triggered NFκBp65 and IκBαphosphorylation as well as decreased cell viability. Together, these data suggest that carbon monoxide-dependent regulation of NO production by the combination of HT with CORM-2 may provide a therapeutic benefit in the treatment of endothelial dysfunction and atherosclerosis.
Microtubule-Associated Proteins in Mesial Temporal Lobe Epilepsy with and without Psychiatric Comorbidities and Their Relation with Granular Cell Layer Dispersion
Authors: Kandratavicius Ludmyla , Monteiro Mariana Raquel , Hallak Jaime Eduardo , Carlotti Carlos Gilberto , Assirati Joao Alberto , Leite Joao Pereira
Published: August 2013

Background. Despite strong association between epilepsy and psychiatric comorbidities, biological substrates are unknown. We have previously reported decreased mossy fiber sprouting in mesial temporal lobe epilepsy (MTLE) patients with psychosis and increased in those with major depression. Microtubule associated proteins (MAPs) are essentially involved in dendritic and synaptic sprouting.Methods. MTLE hippocampi of subjects without psychiatric history, MTLE + major depression, and MTLE + interictal psychosis derived from epilepsy surgery and control necropsies were investigated for neuronal density, granular layer dispersion, and MAP2 and tau immunohistochemistry.Results. Altered MAP2 and tau expression in MTLE and decreased tau expression in MTLE with psychosis were found. Granular layer dispersion correlated inversely with verbal memory scores, and with MAP2 and tau expression in the entorhinal cortex. Patients taking fluoxetine showed increased neuronal density in the granular layer and those taking haloperidol decreased neuronal density in CA3 and subiculum.Conclusions. Our results indicate relations between MAPs, granular layer dispersion, and memory that have not been previously investigated. Differential MAPs expression in human MTLE hippocampi with and without psychiatric comorbidities suggests that psychopathological states in MTLE rely on differential morphological and possibly neurochemical backgrounds. This clinical study was approved by our institution’s Research Ethics Board (HC-FMRP no. 1270/2008) and is registered under the Brazilian National System of Information on Ethics in Human Research (SISNEP) no. 0423.0.004.000-07.
Comparison of Baseline Cepstral Vector and Composite Vectors in the Automatic Seizure Detection Using Probabilistic Neural Networks
Authors: Kamath Chandrakar
Published: August 2013

Epileptic seizures are abnormal sudden discharges in the brain with signatures manifesting in the electroencephalogram (EEG) recordings by frequency changes and increased amplitudes. These changes, in this work, are captured through traditional cepstrum and the cepstrum-derived dynamic features. We compared the performance of the traditional baseline cepstral vector with that of the two composite vectors, the first including velocity cepstral coefficients and the second including velocity and acceleration cepstral coefficients, using probabilistic neural network in general epileptic seizure detection. The comparison is tried on seven different classification problems which encompass all the possible discriminations in the medical field related to epilepsy. In this study, it is found that the overall performance of both the composite vectors deteriorates compared to that of baseline cepstral vector.
Attenuation of Argininosuccinate Lyase Inhibits Cancer Growth via Cyclin A2 and Nitric Oxide
Authors: Huang Hau-Lun , Hsu Hui-Ping , Shieh Shu-Chu , Chang Yung-Sheng , Chen Wei-Ching , Cho Chien-Yu , Teng Chiao-Fang , Su Ih-Jen , Hung Wen-Chun , Lai Ming-Derg
Published: August 2013

Arginine biosynthesis and nitric oxide (NO) production are important for cancer homeostasis. Degradation of arginine may be used to inhibit liver tumors with low argininosuccinate synthetase (ASS) expression. In this report, we investigated an alternative therapeutic approach by targeting argininosuccinate lyase (ASL). ASL is transcriptionally induced by endoplasmic reticulum stress and is overexpressed in some human liver tumors. Knockdown of ASL expression by short hairpin RNA (shRNA) in three liver cancer cell lines, ML-1, HuH-7, and HepG2, decreased colony formation in vitro and tumor growth in vivo. Furthermore, lentiviral infection of ASL shRNA inhibited tumor growth in a therapeutic animal tumor model. Analysis of ASL shRNA on the cell-cycle progression revealed a G2–M delay. Among cell-cycle regulatory molecules, cyclin A2 expression was reduced. Reintroduction of exogenous cyclin A2 restored the cell growth in ASL-knockdown cells. Autophagy was observed in the cells treated with ASL shRNA, as shown by an increase in LC3-II levels and autophagosome formation. The total cellular arginine level was not altered significantly. Inhibition of autophagy further attenuated cell growth, suggesting that autophagy induced by ASL shRNA plays a feedback prosurvival function. Knockdown of ASL reduced NO content, and addition of NO donor partially recovered the growth inhibition by ASL shRNA. In summary, downregulation of ASL attenuated tumor growth and the inhibition was mainly mediated by a decrease of cyclin A2 and NO. Mol Cancer Ther; 12(11); 2505–16. ©2013 AACR.
Role of Slit and Robo Proteins in the Development of Dopaminergic Neurons
Authors: Cornide-Petronio María Eugenia , Barreiro-Iglesias Antón
Published: August 2013

Dopamine plays a number of important roles in the nervous system and the dopaminergic system is affected in several brain disorders. It is therefore of great interest to study the axonal guidance systems that specifically participate in the correct establishment of dopaminergic projections during development and possibly during regenerative processes. In recent years, several reports have shown that Slits and their Robo receptors control the growth of longitudinal (both ascending and descending) mesodiencephalic dopaminergic axons to their appropriate target areas. In vitro studies have shown that Slit1, 2 and 3 are potent repellents of dopamine neurite extension. In vivo studies using both mice and zebrafish mutants for Slits and Robos have shown that Slits and Robos control the lateral and dorsoventral positioning of dopaminergic longitudinal projections during early development. In the present review, we aimed to compile the existing knowledge from both in vitro and in vivo studies on the role of Slit and Robo proteins in the development of dopaminergic neurons as a basis for future studies.
Can COPD Patients Who Hyperinflate During Daily Life Activities Be Identified by Laboratory Tests?
Authors: Lahaije A. , van Helvoort H. , Dekhuijzen R. , Heijdra Y.
Published: August 2013

Background: Identification of patients with chronic obstructive pulmonary disease (COPD) who develop dynamic hyperinflation (DH) during activities in daily life (ADL) is important, because of the association between DH and dyspnea and exercise limitation. Objective: We aimed to answer the question whether measurements of DH during metronome-paced tachypnea (MPT) or cardiopulmonary exercise testing (CPET) can be used to identify patients who develop DH during ADL. Methods: DH was measured by tracking changes in inspiratory capacity during CPET, MPT and ADL. Bland-Altman plots were used to evaluate agreement in DH between methods. With a receiver operating characteristic (ROC) analysis, the overall accuracy of MPT and CPET to identify patients who hyperinflate during ADL was assessed. Results: There are broad limits of agreement in DH between methods. ROC curve analyses showed good overall accuracy of both CPET and MPT to identify patients who hyperinflate during ADL. For CPET, area under the curve (AUC) = 0.956 (95% CI 0.903-1.009). For MPT, AUC = 0.840 (95% CI 0.699-0.981). Sensitivity and specificity to identify patients who hyperinflate during ADL with CPET were 96 and 83%, respectively, and with MPT, they were 89 and 77%, respectively. Conclusion: Both CPET and MPT can serve as screening tools to identify patients who are susceptible to developing DH during ADL. In practice, MPT is the most simple and inexpensive surrogate. However, the sensitivity of MPT is not optimal. When DH does not occur during CPET, it is unlikely to occur during ADL.
Comorbidities and Kidney Transplant Evaluation in the Elderly
Authors: Lenihan Colin R. , Hurley Michael P. , Tan Jane C.
Published: August 2013

Background/Aims: The elderly are the fastest growing subpopulation with end-stage renal disease. The goal of our study was to define characteristics of elderly patients who were considered ineligible for transplantation compared to those who were listed. Methods: 984 patients were referred for evaluation during a 2-year period. Records of patients ≥65 years of age (n = 123) were reviewed. Patients who were listed versus not listed were characterized. Factors associated with waitlisting were determined using standard statistical tools. Results: Half of elderly transplant candidates were accepted for listing compared to 75.4% of those aged <65 years. In multivariable logistic regression, older age (OR 1.29 per year ≥65, 95% CI 1.14-1.45), coronary artery disease (OR 8.57, 95% CI 2.41-30.53), and poor mobility (OR 13.97, 95% CI 4.76-41.00) were independently associated with denial of listing. The receiver operating characteristic curve showed good discrimination for denial of listing (area under the receiver operating characteristic curve of 0.88). Conclusion: Elderly candidates carry a heavy burden of comorbidities and over half of those evaluated are deemed unsuitable for waitlisting. Better delineation of characteristics associated with suitability for transplant candidacy in the elderly is warranted to facilitate appropriate referrals by physicians and management of expectations in potential candidates.