bluuebunny/crossref_metadata_2025 huggingface dataset:
ECMon
Authors: Nagarajan Vijay , Gupta Rajiv
Published: June 2009

The advent of multicores has introduced new challenges for programmers to provide increased performance and software reliability. There has been significant interest in techniques that use software speculation to better utilize the computational power of multicores. At the same time, several recent proposals for ensuring software reliability are not applicable in a multicore setting due to their inability to handle interprocessor shared memory dependences (ISMDs). The demands for performing speculation and ensuring software reliability in a multicore setting, although seemingly different, share a common requirement: the need for monitoring program execution and collecting interprocessor dependence information at low overhead. For example, an important component of speculation is the effcient detection of missspeculation which in turn requires dependence information. Likewise, tasks that help ensure software reliability on multicores, including
recording for replay
, require ISMD information.

In this paper, we propose
ECMon:
support for exposing cache events to the software. This enables the programmer to catch these events and react to them; in effect, efficiently exposing the ISMDs to the programmer. In the context of speculation, we show how
ECMon
optimizes the detection of miss-speculation; we use this simple support to speculate past active barriers and achieve a speedup of 12% for the set of parallel programs considered. As an application of ensuring software reliability, we show how
ECMon
can be used to record shared memory dependences on multicores using no specialized hardware support at only 2.8 fold execution time overhead.
A fault tolerant, area efficient architecture for Shor's factoring algorithm
Authors: Whitney Mark G. , Isailovic Nemanja , Patel Yatish , Kubiatowicz John
Published: June 2009

We optimize the area and latency of Shor's factoring while simultaneously improving fault tolerance through: (1) balancing the use of ancilla generators, (2) aggressive optimization of error correction, and (3) tuning the core adder circuits. Our custom CAD flow produces detailed layouts of the physical components and utilizes simulation to analyze circuits in terms of area, latency, and success probability. We introduce a metric, called ADCR, which is the probabilistic equivalent of the classic Area-Delay product. Our error correction optimization can reduce ADCR by order of magnitude or more. Contrary to conventional wisdom, we show that the area of an optimized quantum circuit is
not
dominated exclusively by error

correction. Further, our adder evaluation shows that quantum carry-lookahead adders (QCLA) beat ripple-carry adders in ADCR, despite being larger and more complex. We conclude with what we believe is one of most accurate estimates of the area and latency required for 1024-bit Shor's factorization: 7659 mm
2
for the smallest circuit and 6 x 10
8
seconds for the fastest circuit.
Performance and power of cache-based reconfigurable computing
Authors: Putnam Andrew , Eggers Susan , Bennett Dave , Dellinger Eric , Mason Jeff , Styles Henry , Sundararajan Prasanna , Wittig Ralph
Published: June 2009

Many-cache is a memory architecture that efficiently supports caching in commercially available FPGAs. It facilitates FPGA programming for high-performance computing (HPC) developers by providing them with memory performance that is greater and power consumption that is less than their current CPU platforms, but without sacrificing their familiar, C-based programming environment.

Many-cache creates multiple, multi-banked caches on top of an FGPA's small, independent memories, each targeting a particular data structure or region of memory in an application and each customized for the memory operations that access it. The caches are automatically generated from C source by the CHiMPS C-to-FPGA compiler.

This paper presents the analyses and optimizations of the CHiMPS compiler that construct many-cache caches. An architectural evaluation of CHiMPS-generated FPGAs demonstrates a performance advantage of 7.8x (geometric mean) over CPU-only execution of the same source code, FPGA power usage that is on average 4.1x less, and consequently performance per watt that is also greater, by a geometric mean of 21.3x.
Flexible reference-counting-based hardware acceleration for garbage collection
Authors: Joao José A. , Mutlu Onur , Patt Yale N.
Published: June 2009

Languages featuring automatic memory management (garbage collection) are increasingly used to write all kinds of applications because they provide clear software engineering and security advantages. Unfortunately, garbage collection imposes a toll on performance and introduces pause times, making such languages less attractive for high-performance or real-time applications. Much progress has been made over the last five decades to reduce the overhead of garbage collection, but it remains significant.

We propose a cooperative hardware-software technique to reduce the performance overhead of garbage collection. The key idea is to reduce the frequency of garbage collection by efficiently detecting and reusing dead memory space in hardware via hardware-implemented reference counting. Thus, even though software garbage collections are still eventually needed, they become much less frequent and have less impact on overall performance. Our technique is compatible with a variety of software garbage collection algorithms, does not break compatibility with existing software, and reduces garbage collection time by 31% on average on the Java DaCapo benchmarks running on the production build of the Jikes RVM, which uses a state-of-the-art generational garbage collector.
Phastlane
Authors: Cianchetti Mark J. , Kerekes Joseph C. , Albonesi David H.
Published: June 2009

Tens and eventually hundreds of processing cores are projected to be integrated onto future microprocessors, making the global interconnect a key component to achieving scalable chip performance within a given power envelope. While CMOS-compatible nanophotonics has emerged as a leading candidate for replacing global wires beyond the 22nm timeframe, on-chip optical interconnect architectures proposed thus far are either limited in scalability or are dependent on comparatively slow electrical control networks.

In this paper, we present Phastlane, a hybrid electrical/optical routing network for future large scale, cache coherent multicore microprocessors. The heart of the Phastlane network is a low-latency optical crossbar that uses simple predecoded source routing to transmit cache-line-sized packets several hops in a single clock cycle under contentionless conditions. When contention exists, the router makes use of electrical buffers and, if necessary, a high speed drop signaling network. Overall, Phastlane achieve 2X better network performance than a state-of-the-art electrical baseline while consuming 80% less network power.
Dynamic performance tuning for speculative threads
Authors: Luo Yangchun , Packirisamy Venkatesan , Hsu Wei-Chung , Zhai Antonia , Mungre Nikhil , Tarkas Ankit
Published: June 2009

In response to the emergence of multicore processors, various novel and sophisticated execution models have been introduced to fully utilize these processors. One such execution model is Thread-Level Speculation (TLS), which allows potentially dependent threads to execute speculatively in parallel. While TLS offers significant performance potential for applications that are otherwise non-parallel, extracting efficient speculative threads in the presence of complex control flow and ambiguous data dependences is a real challenge. This task is further complicated by the fact that the performance of speculative threads is often architecture-dependent, input-sensitive, and exhibits phase behaviors. Thus we propose dynamic performance tuning mechanisms that determine where and how to create speculative threads at runtime.

This paper describes the design, implementation, and evaluation of hardware and software support that takes advantage of runtime performance profiles to extract efficient speculative threads. In our proposed framework, speculative threads are monitored by hardware-based performance counters and their performance impact is estimated. The creation of speculative threads is adjusted based on the estimation. This paper proposes speculative threads performance estimation techniques, that are capable of correctly determining whether speculation can improve performance for loops that corresponds to 83.8% of total loop execution time across all benchmarks. This paper also examines several dynamic performance tuning policies and finds that the best tuning policy achieves an overall speedup of 36.8%on a set of benchmarks from SPEC2000 suite, which outperforms static thread management by 9.5%.
Toward a cloud computing research agenda
Authors: Birman Ken , Chockler Gregory , van Renesse Robbert
Published: June 2009

The 2008 LADIS workshop on Large Scale Distributed Systems brought together leaders from the commercial cloud computing community with researchers working on a variety of topics in distributed computing. The dialog yielded some surprises: some hot research topics seem to be of limited near-term importance to the cloud builders, while some of their practical challenges seem to pose new questions to us as systems researchers. This brief note summarizes our impressions.
Trusting the cloud
Authors: Cachin Christian , Keidar Idit , Shraer Alexander
Published: June 2009

More and more users store data in "clouds" that are accessed remotely over the Internet. We survey well-known cryptographic tools for providing integrity and consistency for data stored in clouds and discuss recent research in cryptography and distributed computing addressing these problems.
A domain-specific approach for software development on Manycore platforms
Authors: Bengtsson Jerker , Svensson Bertil
Published: June 2009

The programming complexity of increasingly parallel processors calls for new tools that assist programmers in utilising the parallel hardware resources. In this paper we present a set of models that we have developed as part of a tool for mapping dataflow graphs onto manycores. One of the models captures the essentials of manycores identified as suitable for signal processing, and which we use as target for our algorithms. As an intermediate representation we introduce timed configuration graphs, which describe the mapping of a model of an application onto a machine model. Moreover, we show how a timed configuration graph by very simple means can be evaluated using an abstract interpretation to obtain performance feedback. This information can be used by our tool and by the programmer in order to discover improved mappings.
On sorting and load balancing on GPUs
Authors: Cederman Daniel , Tsigas Philippas
Published: June 2009

In this paper we take a look at GPU-Quicksort, an efficient Quicksort algorithm suitable for the highly parallel multi-core graphics processors. Quicksort had previously been considered an inefficient sorting solution for graphics processors, but GPU-Quicksort often performs better than the fastest known sorting implementations for graphics processors, such as radix and bitonic sort. Quicksort can thus be seen as a viable alternative for sorting large quantities of data on graphics processors.

We also take look at a comparison of different load balancing schemes. To get maximum performance on the many-core graphics processors it is important to have an even balance of the workload so that all processing units contribute equally to the task at hand. This can be hard to achieve when the cost of a task is not known beforehand and when new sub-tasks are created dynamically during execution. With the recent advent of scatter operations and atomic hardware primitives it is now possible to bring some of the more elaborate dynamic load balancing schemes from the conventional SMP systems domain to the graphics processor domain.
Non-blocking programming on multi-core graphics processors
Authors: Ha Phuong Hoai , Tsigas Philippas , Anshus Otto J.
Published: June 2009

This paper investigates the synchronization power of coalesced memory accesses, a family of memory access mechanisms introduced in recent large multicore architectures like the CUDA graphics processors. We first design three memory access models to capture the fundamental features of the new memory access mechanisms. Subsequently, we prove the exact synchronization power of these models in terms of their consensus numbers. These tight results show that the coalesced memory access mechanisms can facilitate strong synchronization between the threads of multicore processors, without the need of synchronization primitives other than reads and writes.

Moreover, based on the intrinsic features of recent GPU architectures, we construct strong synchronization objects like wait-free and t-resilient read-modify-write objects for a general model of recent GPU architectures without strong hardware synchronization primitives like test-and-set and compare-and-swap. Accesses to the wait-free objects have time complexity O(N), where N is the number of processes. Our result demonstrates that it is possible to construct waitfree synchronization mechanisms for GPUs without the need of strong synchronization primitives in hardware and that wait-free programming is possible for GPUs.
OpenDF
Authors: Bhattacharyya Shuvra S. , Brebner Gordon , Janneck Jörn W. , Eker Johan , von Platen Carl , Mattavelli Marco , Raulet Mickaël
Published: June 2009

This paper presents the OpenDF framework and recalls that dataflow programming was once invented to address the problem of parallel computing. We discuss the problems with an imperative style, von Neumann programs, and present what we believe are the advantages of using a dataflow programming model. The CAL actor language is briefly presented and its role in the ISO/MPEG standard is discussed. The Dataflow Interchange Format (DIF) and related tools can be used for analysis of actors and networks, demonstrating the advantages of a dataflow approach. Finally, an overview of a case study implementing an MPEG- 4 decoder is given.
Scalable directory architecture for distributed shared memory chip multiprocessors
Authors: Fang Huan , Brorsson Mats
Published: June 2009

Traditional Directory-based cache coherence protocol is far from optimal for large-scale cache coherent shared memory multiprocessors due to the increasing latency to access directories stored in DRAM memory. Instead of keeping directories in main memory, we consider distributing the directory together with L2 cache across all nodes on a Chip Multiprocessor. Each node contains a processing unit, a private L1 cache, a slice of L2 cache, memory controller and a router. Both L2 cache and memories are distributed shared and interleaved by a subset of memory address bits. All nodes are interconnected through a low latency two dimensional Mesh network. Directory, being a split component to L2 cache, only stores sharing information for blocks while L2 cache stores only data blocks exclusive with L1 cache. Shared L2 cache can increase total effective cache capacity on chip, but also increase the miss latency when data is on a remote node. Being different from Directory Cache structure, our proposal totally removes the directory from memory, which saves memory space and reduces access latency. Compared to L2 cache that combines directory information internally, our L2 cache structure saves up to 88% cache space and achieves similar performance.
State-space exploration for concurrent algorithms under weak memory orderings
Authors: Jonsson Bengt
Published: June 2009

Several concurrent implementations of familiar data abstractions such as queues, sets, or maps typically do not follow locking disciplines, and often use lock-free synchronization to gain performance. Since such algorithms are exposed to a weak memory model, they are notoriously hard to get correct, as witnessed by many bugs found in published algorithmsWe outline a technique for analyzing correctness of concurrent algorithms under weak memory models, in which a model checker is used to search for correctness violations. The algorithm to be analyzed is transformed into a form where statements may be reordered according to a particular weak memory ordering. The transformed algorithm can then be analyzed by a model-checking tool, e.g., by enumerative state exploration. We illustrate the approach on a small example of a queue, which allows an enqueue operation to be concurrent with a dequeue operation, which we analyze with respect to the RMO memory model defined in SPARC v9.
Model checking race-freeness
Authors: Abdulla Parosh Aziz , Haziza Frédéric , Kindahl Mats
Published: June 2009

With the introduction of highly concurrent systems in standard desktop computers, ensuring correctness of industrial-size concurrent programs is becoming increasingly important. One of the most important standards in use for developing multi-threaded programs is the POSIX Threads standard, commonly known as PThreads. Of particular importance, the analysis of industrial code should, as far as possible, be automatic and not require annotations or other forms of specifications of the code.

Model checking has been one of the most successful approaches to program verification during the last two decades. The size and complexity of applications which can be handled have increased rapidly through integration with symbolic techniques. These methods are designed to work on finite (but large) state spaces. This framework fails to deal with several essential aspects of behaviours for multithreaded programs: there is no bound a priori on the number of threads which may arise in a given run of the system; each thread manipulates local variables which often range over unbounded domains; and the system has a dynamic structure in the sense that threads can be created and killed throughout execution of the system. In this paper we concentrate on checking a particular class of properties for concurrent programs, namely safety properties. In particular, we focus on race-freeness, that is, the absence of race conditions (also known as data races) in shared-variable pthreaded programs.

We will follow a particular methodology which we have earlier developed for model checking general classes of infinite-state systems [1, 3, 6, 8, 9] and apply a symbolic backward reachability analysis to verify the safety property. Since we construct a model as an over-approximation of the original program, proving the safety property in the model implies that the property also holds in the original system. Surprisingly, it leads to a quite efficient analysis which can be carried out fully automatically.
NOBLE
Authors: Sundell Hakan , Tsigas Philippas
Published: June 2009

An essential part of programming for multi-core and multi-processor includes ef cient and reliable means for sharing data. Lock-free data structures are known as very suitable for this purpose, although experienced to be very complex to design. In this paper, we present a software library of non-blocking abstract data types that have been designed to facilitate lock-free programming for non-experts. The system provides: i) ef cient implementations of the most commonly used data types in concurrent and sequential software design, ii) a lock-free memory management system, and iii) a run time-system. The library provides clear semantics that are at least as strong as those of corresponding lock-based implementations of the respective data types. Our software library can be used for facilitating lockfree programming; its design enables the programmer to: i) replace lock-based components of sequential or parallel code easily and ef ciently , ii) use well-tuned concurrent algorithms inside a software or hardware transactional system. In the paper we describe the design and functionality of the system. We also provide experimental results that show that the library can considerably improve the performance of software systems.
LFTHREADS
Authors: Gidenstam Anders , Papatriantafilou Marina
Published: June 2009

This extended abstract presents LFTHREADS, a thread library entirely based on lock-free methods, i.e. no spinlocks or similar synchronization mechanisms are employed in the implementation of the multithreading. Since lockfreedom is highly desirable in multiprocessors/multicores due to its advantages in parallelism, fault-tolerance, convoy-avoidance and more, there is an increased demand in lock-free methods in parallel applications, hence also in multiprocessor/multicore system services. LFTHREADS is the first thread library that provides a lock-free implementation of blocking synchronization primitives for application threads; although the latter may sound like a contradicting goal, such objects have several benefits: e.g. library operations that block and unblock threads on the same synchronization object can make progress in parallel while maintaining the desired thread-level semantics and without having to wait for any "low" operations among them. Besides, as no spin-locks or similar synchronization mechanisms are employed, memory contention can be reduced and processors/cores are able to do useful work. As a consequence, applications, too, can enjoy enhanced parallelism and fault-tolerance. For the synchronization in LFTHREADS we have introduced a new method, which we call responsibility hand-off (RHO), that does not need any special kernel support. The RHO method is also of independent interest, as it can also serve as a tool for lock-free token passing, management of contention and interaction between scheduling and synchronization. This paper gives an outline and the context of LFTHREADS. For more details the reader is refered to [7] and [8].
Wool-A work stealing library
Authors: Faxén Karl-Filip
Published: June 2009

This paper presents some preliminary results on a small light weight user level task management library called Wool. The Wool task scheduler is based on work stealing. The objective of the library is to provide a reasonably convenient programming interface (in particular by not forcing the programmer to write in continuation passing style) in ordinary C while still having a very low task creation overhead. Several task scheduling systems based on work stealing exists, but they are typically either programming languages like Cilk-5 or based on C++ like the Intel TBB or C# as in the Microsoft TPL. Our main conclusions are that such a direct style interface is indeed possible and yields performance that is comparable to that of the Intel TBB.
Methazolamide does not impair respiratory work performance in anesthetized rabbits
Authors: Kiwull-Schöne Heidrun F. , Li Yi , Kiwull Peter J. , Teppema Luc J.
Published: June 2009

In human medicine, the carbonic anhydrase (CA) inhibitor acetazolamide is used to treat irregular breathing disorders. Previously, we demonstrated in the rabbit that this substance stabilized closed-loop gain properties of the respiratory control system, but concomitantly weakened respiratory muscles. Among others, the highly diffusible CA-inhibitor methazolamide differs from acetazolamide in that it fails to activate Ca2+-dependent potassium channels in skeletal muscles. Therefore, we aimed to find out, whether or not methazolamide may exert attenuating adverse effects on respiratory muscle performance as acetazolamide. In anesthetized spontaneously breathing rabbits ( n = 7), we measured simultaneously the CO2 responses of tidal phrenic nerve activity, tidal transpulmonary pressure changes, and tidal volume before and after intravenous application of methazolamide at two mean (± SE) cumulative doses of 3.5 ± 0.1 and 20.8 ± 0.4 mg/kg. Similar to acetazolamide, low- and high-dose methazolamide enhanced baseline ventilation by 52 ± 10% and 166 ± 30%, respectively ( P < 0.01) and lowered the base excess in a dose-dependent manner by up to 8.3 ± 0.9 mmol/l ( P < 0.001). The transmission of a CO2-induced rise in phrenic nerve activity into volume and/or pressure and, hence, respiratory work performance was 0.27 ± 0.05 ml·kg−1·kPa·unit−1 under control conditions, but remained unchanged upon low- or high-dose methazolamide, at 0.30 ± 0.06 and 0.28 ± 0.07 ml·kg−1·kPa·unit−1, respectively. We conclude that methazolamide does not cause respiratory muscle weakening at elevated levels of ventilatory drive. This substance (so far not used for medication of respiratory diseases) may thus exert stabilizing influences on breathing control without adverse effects on respiratory muscle function.
Response Linearity of Alert Monkey Non-Eye Movement Vestibular Nucleus Neurons During Sinusoidal Yaw Rotation
Authors: Newlands Shawn D. , Lin Nan , Wei Min
Published: June 2009

Vestibular afferents display linear responses over a range of amplitudes and frequencies, but comparable data for central vestibular neurons are lacking. To examine the effect of stimulus frequency and magnitude on the response sensitivity and linearity of non-eye movement central vestibular neurons, we recorded from the vestibular nuclei in awake rhesus macaques during sinusoidal yaw rotation at frequencies between 0.1 and 2 Hz and between 7.5 and 210°/s peak velocity. The dynamics of the neurons' responses across frequencies, while holding peak velocity constant, was consistent with previous studies. However, as the peak velocity was varied, while holding the frequency constant, neurons demonstrated lower sensitivities with increasing peak velocity, even at the lowest peak velocities tested. With increasing peak velocity, the proportion of neurons that silenced during a portion of the response increased. However, the decrease in sensitivity of these neurons with higher peak velocities of rotation was not due to increased silencing during the inhibitory portion of the cycle. Rather the neurons displayed peak firing rates that did not increase in proportion to head velocity as the peak velocity of rotation increased. These data suggest that, unlike vestibular afferents, the central vestibular neurons without eye movement sensitivity examined in this study do not follow linear systems principles even at low velocities.
Stimulation of growth and changes in the hepatic transcriptome by 17β-estradiol in the yellow perch (Perca flavescens)
Authors: Goetz Frederick W. , Rise Matthew L. , Rise Marlies , Goetz Giles W. , Binkowski Frederick , Shepherd Brian S.
Published: June 2009

The effects of dietary 17β-estradiol (E2) on growth and liver transcriptomics were investigated in the yellow perch ( Perca flavescens). After a 3-mo treatment, E2significantly stimulated an increase in length and weight of juvenile male and female perch relative to control animals. The increase was significantly greater in females compared with males. Separate, unnormalized cDNA libraries were constructed from equal quantities of RNA from 6 male and 6 female livers of E2-treated and control perch, and 3,546 and 3,719 expressed sequence tags (ESTs) were obtained, respectively. To characterize E2-regulated transcripts, EST frequencies between libraries were calculated within contiguous sequences that were assembled from the combined ESTs of both libraries. Frequencies were also determined in EST transcript groupings produced by aligning all of the ESTs from both libraries at the nucleotide level. From these analyses, there were 28 annotated transcripts that were regulated by 75% between libraries and for which there were at least 5 ESTs of the same transcript between libraries. Regulation of a subset ( 14 ) of these transcripts was confirmed by quantitative reverse transcription-polymerase chain reaction (QPCR). Transcripts that were upregulated by E2included reproduction-related proteins, binding proteins, and proteases and protease inhibitors. While not part of the transcript frequency analysis, QPCR showed significant upregulation of estrogen receptor esr1 and of insulin-like growth factor I (IGF-I) in E2livers. E2-downregulated transcripts represented a variety of functional categories including components of the respiratory chain, lipid transport and metabolism, glycolysis, amino acid and nitrogen metabolism, binding proteins, a hydrolytic enzyme, and a transcriptional regulator. In perch it appears that exogenous estrogen drastically shifts liver metabolism toward the production of lipoproteins and carbohydrate binding proteins, and that the growth-promoting action may involve an increase in hepatic IGF-I production.
Physiological and toxicological transcriptome changes in HepG2 cells exposed to copper
Authors: Song Min Ok , Li Jianying , Freedman Jonathan H.
Published: June 2009

Copper is an essential trace element; however, at supraphysiological levels, it can be extremely toxic. Microarray data from HepG2 cells exposed to 100, 200, 400, and 600 μM copper for 4, 8, 12 and 24 h were generated and analyzed. Principal components, K-means, and hierarchical clustering, interactome, and pathway mapping analyses indicated that these exposure conditions induce physiological and toxicological changes in the HepG2 transcriptome. As a general trend, when the level of toxicity increases, the number and diversity of affected genes, Gene Ontology categories, regulatory pathways, and complexity of interactomes increase. Physiological responses to copper include transition metal ion binding and responses to stress/stimulus, whereas toxicological responses include apoptosis, morphogenesis, and negative regulation of biomolecule metabolism. The global gene expression profile was overlaid onto biomolecular interaction networks and signal transduction cascades using pathway mapping and interactome identification. This analysis indicated that copper modulates signal transduction pathways associated with MAPK, NF-κB, death receptor, IGF-I, hypoxia, IL-10, IL-2, IL-6, EGF, Toll-like receptor, protein ubiquitination, xenobiotic metabolism, leukocyte extravasation, complement and coagulation, and sonic hedgehog signaling. These results provide insights into the global and molecular mechanisms regulating the physiological and toxicological responses to metal exposure.
Ovarian Teratoma Masquerading as a CSF Pseudocyst in a Female with a Ventriculoperitoneal Shunt
Authors: Mislow John M. K. , Slotkin Jonathan R. , Proctor Mark R.
Published: June 2009

Background. In today's fast-paced and high-acuity emergency departments, clinicians are often compelled to triage cases so rapidly that a differential diagnosis consistent with the history and physical examination is not comprehensive.Case Report. This case report describes the unexpected finding of a cystic ovarian neoplasm in a young female with an abdominal mass and a ventriculoperitoneal shunt, initially diagnosed as a cerebrospinal fluid pseudocyst. We use this case to illustrate that the astute clinician must always synthesize a diagnosis from all data sources and not to rely on initial radiographic evaluations.Conclusions. This remarkable case demonstrates that all differential diagnoses must be entertained in order to rapidly and accurately diagnose a patient with a cystic abdominal mass.
Changes in EEG Power Spectral Density and Cortical Connectivity in Healthy and Tetraplegic Patients during a Motor Imagery Task
Authors: Cona Filippo , Zavaglia Melissa , Astolfi Laura , Babiloni Fabio , Ursino Mauro
Published: June 2009

Knowledge of brain connectivity is an important aspect of modern neuroscience, to understand how the brain realizes its functions. In this work, neural mass models including four groups of excitatory and inhibitory neurons are used to estimate the connectivity among three cortical regions of interests (ROIs) during a foot‐movement task. Real data were obtained via high‐resolution scalp EEGs on two populations: healthy volunteers and tetraplegic patients. A 3‐shell Boundary Element Model of the head was used to estimate the cortical current density and to derive cortical EEGs in the three ROIs.
The model assumes that each ROI can generate an intrinsic rhythm in the beta range, and receives rhythms in the alpha and gamma ranges from other two regions. Connectivity strengths among the ROIs were estimated by means of an original genetic algorithm that tries to minimize several cost functions of the difference between real and model power spectral densities. Results show that the stronger connections are those from the cingulate cortex to the primary and supplementary motor areas, thus emphasizing the pivotal role played by the CMA_L during the task. Tetraplegic patients exhibit higher connectivity strength on average, with significant statistical differences in some connections. The results are commented and virtues and limitations of the proposed method discussed.
Nonlinear Dynamics and Chaos in a Fractional‐Order HIV Model
Authors: Ye Haiping , Ding Yongsheng
Published: June 2009

We introduce fractional order into an HIV model. We consider
the effect of viral diversity on the human immune system with frequency dependent rate of proliferation of cytotoxic T‐lymphocytes (CTLs) and rate of
elimination of infected cells by CTLs, based on a fractional‐order differential
equation model. For the one‐virus model, our analysis shows that the interior
equilibrium which is unstable in the classical integer‐order model can become
asymptotically stable in our fractional‐order model and numerical simulations
confirm this. We also present simulation results of the chaotic behaviors produced from the fractional‐order HIV model with viral diversity by using an
Adams‐type predictor‐corrector method.
Breast Angiosarcoma Metastatic to the Ovary
Authors: Souza Frederico F. , Katkar Amol , den Abbeele Annick D. Van , Dipiro Pamela J.
Published: June 2009

Ovarian masses are common findings in general gynecological practice. Approximately 5%–10% of ovarian malignancies are diagnosed as metastatic tumors. Primary angiosarcoma can arise anywhere in the body and when it arises in the breast, it usually affects women in their 3rd and 4th decades and accounts for one in 1700–2300 cases of primary breast cancer. Although unusual, breast angiosarcomas tend to metastasize hematogenously rather than lymphogenously, have high rates of local recurrence, that often develop metastases soon after treatment, and have a dismal prognosis. We present a case of a solitary ovarian metastasis from angiosarcoma of the breast.
Approximate Algorithm for Determining Pulse Edges of a PWM Inverter Based on Natural Sampling
Authors: Kostić Dragutin , Šinik Vladimir
Published: June 2009

The paper presents a new algorithm for determination of pulse edges of a modulated wave of a PWM voltage inverter which offers a possibility that natural sampling is realized with an arbitrary accuracy without applying an iterative procedure. The basic idea is to express the angles which determine pulse edges of the modulated signal as polynomials of amplitude modulation index. Geometric interpretation of sampling of the polynomial algorithm is identical with the geometric interpretation of natural algorithm, but the transcendental equation whose solution defines pulse edges of the modulated signal is replaced by a simple procedure of finding values of a polynomial whose coefficients are determined in advance by an exact procedure. This approach gives the possibility of digital implementation of polynomial sampling method using the low‐cost microprocessor platforms.
Parameter Estimation for Partial Differential Equations by Collage‐Based Numerical Approximation
Authors: Deng Xiaoyan , Liao Qingxi
Published: June 2009

The inverse problem of using measurements to estimate unknown parameters of a system often arises in engineering practice and scientific research. This paper proposes a Collage‐based parameter inversion framework for a class of partial differential equations. The Collage method is used to convert the parameter estimation inverse problem
into a minimization problem of a function of several variables after the partial differential equation is approximated by a differential dynamical system. Then numerical schemes for solving this minimization problem are proposed, including grid approximation and ant colony optimization. The proposed schemes are applied to a parameter estimation problem for the Belousov‐Zhabotinskii equation, and the results show that the proposed approximation method is efficient for both linear and nonlinear partial differential equations with respect to unknown parameters. At worst, the presented method provides an excellent starting point for traditional inversion methods that must first select a good starting point.
Sequentially Adapted Parallel Feedforward Active Noise Control of Noisy Sinusoidal Signals
Authors: Kannan Govind , Panahi Issa M. S. , Briggs Richard W.
Published: June 2009

A large class of acoustic noise sources has an underlying periodic process that generates a periodic noise component, and thus their acoustic noise can in general be modeled as the sum of a periodic signal and a randomly fluctuating signal (usually a broadband background noise). Active control of periodic noise (i.e., for a mixture of sinusoids) is more effective than that of random noise. For mixtures of sinusoids in a background broadband random noise, conventional FXLMS‐based single filter method does not reach the maximum achievable Noise Attenuation Level (NALmax ). In this paper, an alternative approach is taken and the idea of a parallel active noise control (ANC) architecture for cancelling mixtures of periodic and random signals is presented. The proposed ANC system separates the noise into periodic and random components and generates corresponding antinoises via separate noise cancelling filters, and tends to reach NALmax  consistently. The derivation of NALmax  is presented. Both the separation and noise cancellation are based on adaptive filtering. Experimental results verify the analytical development by showing superior performance of the proposed method, over the single‐filter approach, for several cases of sinusoids in white noise.
Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST‐SSR Markers and Gene Discovery
Authors: Guo Baozhu , Chen Xiaoping , Hong Yanbin , Liang Xuanqiang , Dang Phat , Brenneman Tim , Holbrook Corley , Culbreath Albert
Published: June 2009

Peanut is vulnerable to a range of foliar diseases such as spotted wilt caused by Tomato spotted wilt virus (TSWV), early (Cercospora arachidicola) and late (Cercosporidium personatum) leaf spots, southern stem rot (Sclerotium rolfsii), and sclerotinia blight (Sclerotinia minor). In this study, we report the generation of 17,376 peanut expressed sequence tags (ESTs) from leaf tissues of a peanut cultivar (Tifrunner, resistant to TSWV and leaf spots) and a breeding line (GT‐C20, susceptible to TSWV and leaf spots). After trimming vector and discarding low quality sequences, a total of 14,432 high‐quality ESTs were selected for further analysis and deposition to GenBank. Sequence clustering resulted in 6,888 unique ESTs composed of 1,703 tentative consensus (TCs) sequences and 5185 singletons. A large number of ESTs (5717) representing genes of unknown functions were also identified. Among the unique sequences, there were 856 EST‐SSRs identified. A total of 290 new EST‐based SSR markers were developed and examined for amplification and polymorphism in cultivated peanut and wild species. Resequencing information of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the SSR regions. In addition, a few additional INDEL mutations and substitutions were observed in the regions flanking the microsatellite regions. In addition, some defense‐related transcripts were also identified, such as putative oxalate oxidase (EU024476) and NBS‐LRR domains. EST data in this study have provided a new source of information for gene discovery and development of SSR markers in cultivated peanut. A total of 16931 ESTs have been deposited to the NCBI GenBank database with accession numbers ES751523 to
ES768453.
Frequency‐Domain Robust Performance Condition for Controller Uncertainty in SISO LTI Systems: A Geometric Approach
Authors: Raissi Dehkordi Vahid , Boulet Benoit
Published: June 2009

This paper deals with the robust performance problem of a linear time‐invariant control system in the presence of robust controller uncertainty. Assuming that plant uncertainty is modeled as an additive perturbation, a geometrical approach is followed in order to find a necessary and sufficient condition for robust performance in the form of a bound on the magnitude of controller uncertainty. This frequency domain bound is derived by converting the problem into an optimization problem, whose solution is shown to be more time‐efficient than a conventional structured singular value calculation. The bound on controller uncertainty can be used in controller order reduction and implementation problems.
Comprehensive and Rapid Real-Time PCR Analysis of 21 Foodborne Outbreaks
Authors: Fukushima Hiroshi , Katsube Kazunori , Tsunomori Yoshie , Kishi Ryoko , Atsuta Junko , Akiba Yuko
Published: June 2009

A set of four duplex SYBR Green I PCR (SG-PCR) assay combined with DNA extraction using QIAamp DNA Stool Mini kit was evaluated for the detection of foodborne bacteria from 21 foodborne outbreaks. The causative pathogens were detected in almost all cases in 2 hours or less. The first run was for the detection of 8 main foodborne pathogens in 5 stool specimens within 2 hours and the second run was for the detection of other unusual suspect pathogens within a further 45 minutes. After 2 to 4 days, the causative agents were isolated and identified. The results proved that for comprehensive and rapid molecular diagnosis in foodborne outbreaks, Duplex SG-PCR assay is not only very useful, but is also economically viable for one-step differentiation of causative pathogens in fecal specimens obtained from symptomatic patients. This then allows for effective diagnosis and management of foodborne outbreaks.
Signatures of Depression in Non‐Stationary Biometric Time Series
Authors: Culic Milka , Gjoneska Biljana , Hinrikus Hiie , Jändel Magnus , Klonowski Wlodzimierz , Liljenström Hans , Pop-Jordanova Nada , Psatta Dan , von Rosen Dietrich , Wahlund Björn
Published: June 2009

This paper is based on a discussion that was held during a special session on models of mental disorders, at the NeuroMath meeting in Stockholm, Sweden, in September 2008. At this occasion, scientists from different countries and different fields of research presented their research and discussed open questions with regard to analyses and models of mental disorders, in particular depression. The content of this paper emerged from these discussions and in the presentation we briefly link biomarkers (hormones), bio‐signals (EEG) and biomaps (brain‐maps via EEG) to depression and its treatments, via linear statistical models as well as nonlinear dynamic models. Some examples involving EEG‐data are presented.
Multiple Histology Phase II Trials
Authors: LeBlanc Michael , Rankin Cathryn , Crowley John
Published: June 2009

Purpose: Testing agents in cancers with multiple disease subtypes, in which the activity of a new treatment may vary between subtypes, presents statistical and logistical challenges. We propose a flexible phase II strategy which includes both analyses for each histology or stratum and a combined analysis which borrows information from all the patients in the study. Sequential futility analyses are conducted once each subgroup or the overall group reaches a specified minimum accrual.

Experimental Design: Examples based on a soft tissue sarcoma phase II trial, which includes multiple histologies and simulation studies, are used to assess the statistical properties of the proposed strategy.

Results: The combined analyses in one phase II trial lead to smaller expected sample sizes when the drug is broadly inactive, and to greater statistical power if there is modest activity across multiple strata as compared with conducting several smaller phase II studies. In addition, by retaining the stratum-specific tests, the design allows the identification of subgroups for which the agents are most active.

Conclusion: To consider phase II testing with multiple biological subtypes, a strategy which combines both the individual subgroup tests and overall combined tests has promising statistical properties. Our results support the appropriate use of statistical borrowing of information in phase II studies in this setting. More broadly, this work fits the paradigm that phase II studies should include as broad a group of patients as scientifically reasonable, but incorporate design considerations for subsets of patients with potentially differing responses to therapy.
Disclosure of Research Results from Cancer Genomic Studies: State of the Science
Authors: Dressler Lynn G.
Published: June 2009

Although the cancer research community has supported a “nondisclosure” position about the return of individual results to research subjects, new technologies, such as genome wide association studies, will reveal clinically relevant findings, some of which cannot be ignored. What recommendations exist that can guide researchers and Institutional Review Boards (IRBs) about this issue? This article summarizes the relevant public documents about the disclosure of individual research results to inform policy development. Four stakeholder groups were selected to make this comparison: federal, professional, advisory, and advocacy groups. Regardless of a group's position on disclosure, there was consensus that if research results were to be disclosed under any condition, the results must be analytically and clinically validated and that the researcher should not make this decision alone, but in conjunction with the IRB. There was no consensus, however, on the specific determinants for disclosure or what constitutes clinical validity. Although sufficient agreement exists to begin developing general guidelines about the process for disclosure of individual research results, the actual determinants with which to guide this decision remain challenging. An alternate framework that addresses the threshold of uncertainty a stakeholder is willing to accept, the positive predictive value of the research finding, and the magnitude of harm of returning results may be more effective to guide decision making. These assessments, along with what is considered useful information, requires the involvement of the research subject community to inform decision-making and move the policy process forward.