Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.

Microarrays containing 1046 human cDNAs of unknown sequence were printed on glass with high-speed robotics. These 1.0-cm2 DNA "chips" were used to quantitatively monitor differential expression of the cognate human genes using a highly sensitive two-color hybridization assay. Array elements that displayed differential expression patterns under given experimental conditions were characterized by sequencing. The identification of known and novel heat shock and phorbol ester-regulated genes in human T cells demonstrates the sensitivity of the assay. Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery.

Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.

A number of studies have noted that nucleotide substitution rates at the chloroplast-encoded rbcL locus violate the molecular clock principle. Substitution rate variation at this plastid gene is particularly pronounced between palms and grasses; for example, a previous study estimated that substitution rates in rbcL sequences are approximately 5-fold faster in grasses than in palms. To determine whether a proportionate change in substitution rates also occurs in plant nuclear genes, we characterized nucleotide substitution rates in palm and grass sequences for the nuclear gene Adh. In this article, we report that palm sequences evolve at a rate of 2.61 x 10(-9) substitution per synonymous site per year, a rate which is slower than most plant nuclear genes. Grass Adh sequences evolve approximately 2.5-fold faster than palms at synonymous sites. Thus, synonymous rates in nuclear Adh genes show a marked decrease in palms relative to grasses, paralleling the pattern found at the plastid rbcL locus. This shared pattern indicates that synonymous rates are correlated between a nuclear and a plastid gene. Remarkably, nonsynonymous rates do not show this correlation. Nonsynonymous rates vary between two duplicated grass Adh loci, and nonsynonymous rates at the palm Adh locus are not markedly reduced relative to grasses.

Studies of the lamin proteinase reveal multiple parallel biochemical pathways during apoptotic execution.

Although specific proteinases play a critical role in the active phase of apoptosis, their substrates are largely unknown. We previously identified poly(ADP-ribose) polymerase (PARP) as an apoptosis-associated substrate for proteinase(s) related to interleukin 1 beta-converting enzyme (ICE). Now we have used a cell-free system to characterize proteinase(s) that cleave the nuclear lamins during apoptosis. Lamin cleavage during apoptosis requires the action of a second ICE-like enyzme, which exhibits kinetics of cleavage and a profile of sensitivity to specific inhibitors that is distinct from the PARP proteinase. Thus, multiple ICE-like enzymes are required for apoptotic events in these cell-free extracts. Inhibition of the lamin proteinase with tosyllysine "chloromethyl ketone" blocks nuclear apoptosis prior to the packaging of condensed chromatin into apoptotic bodies. Under these conditions, the nuclear DNA is fully cleaved to a nucleosomal ladder. Our studies reveal that the lamin proteinase and the fragmentation nuclease function in independent parallel pathways during the final stages of apoptotic execution. Neither pathway alone is sufficient for completion of nuclear apoptosis. Instead, the various activities cooperate to drive the disassembly of the nucleus.

Microevolutionary responses in experimental populations of plants to CO2-enriched environments: parallel results from two model systems.

Despite the critical role that terrestrial vegetation plays in the Earth's carbon cycle, very little is known about the potential evolutionary responses of plants to anthropogenically induced increases in concentrations of atmospheric CO2. We present experimental evidence that rising CO2 concentration may have a direct impact on the genetic composition and diversity of plant populations but is unlikely to result in selection favoring genotypes that exhibit increased productivity in a CO2-enriched atmosphere. Experimental populations of an annual plant (Abutilon theophrasti, velvetleaf) and a temperate forest tree (Betula alleghaniensis, yellow birch) displayed responses to increased CO2 that were both strongly density-dependent and genotype-specific. In competitive stands, a higher concentration of CO2 resulted in pronounced shifts in genetic composition, even though overall CO2-induced productivity enhancements were small. For the annual species, quantitative estimates of response to selection under competition were 3 times higher at the elevated CO2 level. However, genotypes that displayed the highest growth responses to CO2 when grown in the absence of competition did not have the highest fitness in competitive stands. We suggest that increased CO2 intensified interplant competition and that selection favored genotypes with a greater ability to compete for resources other than CO2. Thus, while increased CO2 may enhance rates of selection in populations of competing plants, it is unlikely to result in the evolution of increased CO2 responsiveness or to operate as an important feedback in the global carbon cycle. However, the increased intensity of selection and drift driven by rising CO2 levels may have an impact on the genetic diversity in plant populations.

Convergent and parallel activation of low-conductance potassium channels by calcium and cAMP-dependent protein kinase.

K+ channels, which have been linked to regulation of electrogenic solute transport as well as Ca2+ influx, represent a locus in hepatocytes for the concerted actions of hormones that employ Ca2+ and cAMP as intracellular messengers. Despite considerable study, the single-channel basis for synergistic effects of Ca2+ and cAMP on hepatocellular K+ conductance is not well understood. To address this question, patch-clamp recording techniques were applied to a model liver cell line, HTC hepatoma cells. Increasing the cytosolic Ca2+ concentration ([Ca2+]i) in HTC cells, either by activation of purinergic receptors with ATP or by inhibition of intracellular Ca2+ sequestration with thapsigargin, activated low-conductance (9-pS) K+ channels. Studies with excised membrane patches suggested that these channels were directly activated by Ca2+. Exposure of HTC cells to a permeant cAMP analog, 8-(4-chlorophenylthio)-cAMP, also activated 9-pS K+ channels but did not change [Ca2+]i. In excised membrane patches, cAMP-dependent protein kinase (the downstream effector of cAMP) activated K+ channels with conductance and selectivity identical to those of channels activated by Ca2+. In addition, cAMP-dependent protein kinase activated a distinct K+ channel type (5 pS). These data represent the differential regulation of low-conductance K+ channels by signaling pathways mediated by Ca2+ and cAMP. Moreover, since low-conductance Ca(2+)-activated K+ channels have been identified in a variety of cell types, these findings suggest that differential regulation of K+ channels by hormones with distinct signaling pathways may provide a mechanism for hormonal control of solute transport and Ca(2+)-dependent cellular functions in the liver as well as other nonexcitable tissues.

Neurosecretory habituation in PC12 cells: modulation during parallel habituation.

PC12 cells habituate during repetitive stimulation with acetylcholine, bradykinin, or high potassium. Interspersing these stimulants did not affect the rate of habituation of the others, but it could modulate the amplitude of the norepinephrine secretion each could achieve. Stimulation with acetylcholine inhibited norepinephrine secretion caused by high potassium and bradykinin stimulation, while high potassium had no effect on acetylcholine or bradykinin, and bradykinin increased secretion caused by acetylcholine. Changes in norepinephrine secretion resulting from any of these stimulants correlated with changes in internal calcium levels. Cyclic AMP-, protein kinase C-, and calmodulin-dependent second messenger pathways all modulated norepinephrine secretion caused by acetylcholine and high potassium and showed a distinct hierarchy in their effectiveness. These data demonstrate that different receptor pathways can change the norepinephrine response of one another while not changing the levels of the molecules responsible for habituation.

Reconfigurable computing for Monte Carlo simulations: results and prospects of the Janus project

We describe Janus, a massively parallel FPGA-based computer optimized for the simulation of spin glasses, theoretical models for the behavior of glassy materials. FPGAs (as compared to GPUs or many-core processors) provide a complementary approach to massively parallel computing. In particular, our model problem is formulated in terms of binary variables, and floating-point operations can be (almost) completely avoided. The FPGA architecture allows us to run many independent threads with almost no latencies in memory access, thus updating up to 1024 spins per cycle. We describe Janus in detail and we summarize the physics results obtained in four years of operation of this machine; we discuss two types of physics applications: long simulations on very large systems (which try to mimic and provide understanding about the experimental non equilibrium dynamics), and low-temperature equilibrium simulations using an artificial parallel tempering dynamics. The time scale of our non-equilibrium simulations spans eleven orders of magnitude (from picoseconds to a tenth of a second). On the other hand, our equilibrium simulations are unprecedented both because of the low temperatures reached and for the large systems that we have brought to equilibrium. A finite-time scaling ansatz emerges from the detailed comparison of the two sets of simulations. Janus has made it possible to perform spin glass simulations that would take several decades on more conventional architectures. The paper ends with an assessment of the potential of possible future versions of the Janus architecture, based on state-of-the-art technology.

High-speed polynomial basis multipliers over GF(2(m)) for special pentanomial.

Efficient hardware implementations of arithmetic operations in the Galois field are highly desirable for several applications, such as coding theory, computer algebra and cryptography. Among these operations, multiplication is of special interest because it is considered the most important building block. Therefore, high-speed algorithms and hardware architectures for computing multiplication are highly required. In this paper, bit-parallel polynomial basis multipliers over the binary field GF(2(m)) generated using type II irreducible pentanomials are considered. The multiplier here presented has the lowest time complexity known to date for similar multipliers based on this type of irreducible pentanomials.

Um método de otimização da relação desempenho/consumo de energia para arquiteturas multi-cores heterogêneas em FPGA

Devido às tendências de crescimento da quantidade de dados processados e a crescente necessidade por computação de alto desempenho, mudanças significativas estão acontecendo no projeto de arquiteturas de computadores. Com isso, tem-se migrado do paradigma sequencial para o paralelo, com centenas ou milhares de núcleos de processamento em um mesmo chip. Dentro desse contexto, o gerenciamento de energia torna-se cada vez mais importante, principalmente em sistemas embarcados, que geralmente são alimentados por baterias. De acordo com a Lei de Moore, o desempenho de um processador dobra a cada 18 meses, porém a capacidade das baterias dobra somente a cada 10 anos. Esta situação provoca uma enorme lacuna, que pode ser amenizada com a utilização de arquiteturas multi-cores heterogêneas. Um desafio fundamental que permanece em aberto para estas arquiteturas é realizar a integração entre desenvolvimento de código embarcado, escalonamento e hardware para gerenciamento de energia. O objetivo geral deste trabalho de doutorado é investigar técnicas para otimização da relação desempenho/consumo de energia em arquiteturas multi-cores heterogêneas single-ISA implementadas em FPGA. Nesse sentido, buscou-se por soluções que obtivessem o melhor desempenho possível a um consumo de energia ótimo. Isto foi feito por meio da combinação de mineração de dados para a análise de softwares baseados em threads aliadas às técnicas tradicionais para gerenciamento de energia, como way-shutdown dinâmico, e uma nova política de escalonamento heterogeneity-aware. Como principais contribuições pode-se citar a combinação de técnicas de gerenciamento de energia em diversos níveis como o nível do hardware, do escalonamento e da compilação; e uma política de escalonamento integrada com uma arquitetura multi-core heterogênea em relação ao tamanho da memória cache L1.

An hybrid parallel algorithm for solving tridiagonal linear systems versus the Wang’s method in a Cray T3D BSP computer

In this paper we describe an hybrid algorithm for an even number of processors based on an algorithm for two processors and the Overlapping Partition Method for tridiagonal systems. Moreover, we compare this hybrid method with the Partition Wang’s method in a BSP computer. Finally, we compare the theoretical computation cost of both methods for a Cray T3D computer, using the cost model that BSP model provides.

Sequential and parallel synchronous alternating iterative methods

The so-called parallel multisplitting nonstationary iterative Model A was introduced by Bru, Elsner, and Neumann [Linear Algebra and its Applications 103:175-192 (1988)] for solving a nonsingular linear system Ax = b using a weak nonnegative multisplitting of the first type. In this paper new results are introduced when A is a monotone matrix using a weak nonnegative multisplitting of the second type and when A is a symmetric positive definite matrix using a P -regular multisplitting. Also, nonstationary alternating iterative methods are studied. Finally, combining Model A and alternating iterative methods, two new models of parallel multisplitting nonstationary iterations are introduced. When matrix A is monotone and the multisplittings are weak nonnegative of the first or of the second type, both models lead to convergent schemes. Also, when matrix A is symmetric positive definite and the multisplittings are P -regular, the schemes are also convergent.

A parallel method for impulsive image noise removal on hybrid CPU/GPU systems

A parallel algorithm for image noise removal is proposed. The algorithm is based on peer group concept and uses a fuzzy metric. An optimization study on the use of the CUDA platform to remove impulsive noise using this algorithm is presented. Moreover, an implementation of the algorithm on multi-core platforms using OpenMP is presented. Performance is evaluated in terms of execution time and a comparison of the implementation parallelised in multi-core, GPUs and the combination of both is conducted. A performance analysis with large images is conducted in order to identify the amount of pixels to allocate in the CPU and GPU. The observed time shows that both devices must have work to do, leaving the most to the GPU. Results show that parallel implementations of denoising filters on GPUs and multi-cores are very advisable, and they open the door to use such algorithms for real-time processing.

Parallel Computational Intelligence-Based Multi-Camera Surveillance System

In this work, we present a multi-camera surveillance system based on the use of self-organizing neural networks to represent events on video. The system processes several tasks in parallel using GPUs (graphic processor units). It addresses multiple vision tasks at various levels, such as segmentation, representation or characterization, analysis and monitoring of the movement. These features allow the construction of a robust representation of the environment and interpret the behavior of mobile agents in the scene. It is also necessary to integrate the vision module into a global system that operates in a complex environment by receiving images from multiple acquisition devices at video frequency. Offering relevant information to higher level systems, monitoring and making decisions in real time, it must accomplish a set of requirements, such as: time constraints, high availability, robustness, high processing speed and re-configurability. We have built a system able to represent and analyze the motion in video acquired by a multi-camera network and to process multi-source data in parallel on a multi-GPU architecture.

Real time motion estimation using a neural architecture implemented on GPUs

This work describes a neural network based architecture that represents and estimates object motion in videos. This architecture addresses multiple computer vision tasks such as image segmentation, object representation or characterization, motion analysis and tracking. The use of a neural network architecture allows for the simultaneous estimation of global and local motion and the representation of deformable objects. This architecture also avoids the problem of finding corresponding features while tracking moving objects. Due to the parallel nature of neural networks, the architecture has been implemented on GPUs that allows the system to meet a set of requirements such as: time constraints management, robustness, high processing speed and re-configurability. Experiments are presented that demonstrate the validity of our architecture to solve problems of mobile agents tracking and motion analysis.

Parallel relaxed and extrapolated algorithms for computing PageRank

In this paper, parallel Relaxed and Extrapolated algorithms based on the Power method for accelerating the PageRank computation are presented. Different parallel implementations of the Power method and the proposed variants are analyzed using different data distribution strategies. The reported experiments show the behavior and effectiveness of the designed algorithms for realistic test data using either OpenMP, MPI or an hybrid OpenMP/MPI approach to exploit the benefits of shared memory inside the nodes of current SMP supercomputers.