Parallel pipelined array architectures for real-time histogram computation in consumer devices

The real-time parallel computation of histograms using an array of pipelined cells is proposed and prototyped in this paper with application to consumer imaging products. The array operates in two modes: histogram computation and histogram reading. The proposed parallel computation method does not use any memory blocks. The resulting histogram bins can be stored into an external memory block in a pipelined fashion for subsequent reading or streaming of the results. The array of cells can be tuned to accommodate the required data path width in a VLSI image processing engine as present in many imaging consumer devices. Synthesis of the architectures presented in this paper in FPGA are shown to compute the real-time histogram of images streamed at over 36 megapixels at 30 frames/s by processing in parallel 1, 2 or 4 pixels per clock cycle.

Abstract platforms of computation

Computational formalisms have been pushing the boundaries of the field of computing for the last 80 years and much debate has surrounded what computing entails; what it is, and what it is not. This paper seeks to explore the boundaries of the ideas of computation and provide a framework for enabling a constructive discussion of computational ideas. First, a review of computing is given, ranging from Turing Machines to interactive computing. Then, a variety of natural physical systems are considered for their computational qualities. From this exploration, a framework is presented under which all dynamical systems can be considered as instances of the class of abstract computational platforms. An abstract computational platform is defined by both its intrinsic dynamics and how it allows computation that is meaningful to an external agent through the configuration of constraints upon those dynamics. It is asserted that a platform’s computational expressiveness is directly related to the freedom with which constraints can be placed. Finally, the requirements for a formal constraint description language are considered and it is proposed that Abstract State Machines may provide a reasonable basis for such a language.

Improving CS-4 user data rate in GPRS enabled devices by using a BLER co-processor

The General Packet Radio Service (GPRS) was developed to allow packet data to be transported efficiently over an existing circuit switched radio network. The main applications for GPRS are in transporting IP datagram’s from the user’s mobile Internet browser to and from the Internet, or in telemetry equipment. A simple Error Detection and Correction (EDC) scheme to improve the GPRS Block Error Rate (BLER) performance is presented, particularly for coding scheme 4 (CS-4), however gains in other coding schemes are seen. For every GPRS radio block that is corrected by the EDC scheme, the block does not need to be retransmitted releasing bandwidth in the channel, improving throughput and the user’s application data rate. As GPRS requires intensive processing in the baseband, a viable hardware solution for a GPRS BLER co-processor is discussed that has been currently implemented in a Field Programmable Gate Array (FPGA) and presented in this paper.

Rational modification of the hierarchy of intermolecular interactions in molecular crystal structures by using tunable halogen bonds

A family of 16 isomolecular salts (3-XpyH)(2)[MX'(4)] (3-XpyH=3-halopyridinium; M=Co, Zn; X=(F), Cl, Br, (I); X'=Cl, Br, I) each containing rigid organic cations and tetrahedral halometallate anions has been prepared and characterized by X-ray single crystal and/or powder diffraction. Their crystal structures reflect the competition and cooperation between non-covalent interactions: N-H center dot center dot center dot X'-M hydrogen bonds, C-X center dot center dot center dot X'-M halogen bonds and pi-pi stacking. The latter are essentially unchanged in strength across the series, but both halogen bonds and hydrogen bonds are modified in strength upon changing the halogens involved. Changing the organic halogen (X) from F to I strengthens the C-X center dot center dot center dot X'-M halogen bonds, whereas an analogous change of the inorganic halogen (X') weakens both halogen bonds and N-H center dot center dot center dot X'-M hydrogen bonds. By so tuning the strength of the putative halogen bonds from repulsive to weak to moderately strong attractive interactions, the hierarchy of the interactions has been modified rationally leading to systematic changes in crystal packing. Three classes of crystal structure are obtained. In type A (C-F center dot center dot center dot X'-M) halogen bonds are absent. The structure is directed by N-H center dot center dot center dot X'-M hydrogen bonds and pi-stacking interactions. In type B structures, involving small organic halogens (X) and large inorganic halogens (X'), long (weak) C-X center dot center dot center dot X'-M interactions are observed with type I halogen-halogen interaction geometries (C-X center dot center dot center dot X' approximate to X center dot center dot center dot X'-M approximate to 155 degrees), but hydrogen bonds still dominate. Thus, minor but quite significant perturbations from the type A structure arise. In type C, involving larger organic halogens (X) and smaller inorganic halogens (X'), stronger halogen bonds are formed with a type II halogen-halogen interaction geometry (C-X center dot center dot center dot X' approximate to 180 degrees; X center dot center dot center dot X'-M approximate to 110 degrees) that is electrostatically attractive. The halogen bonds play a major role alongside hydrogen bonds in directing the type C structures, which as a result are quite different from type A and B.

Cross-modal preference acquisition: evaluative conditioning of pictures by affective olfactory and auditory cues

In this research, a cross-model paradigm was chosen to test the hypothesis that affective olfactory and auditory cues paired with neutral visual stimuli bearing no resemblance or logical connection to the affective cues can evoke preference shifts in those stimuli. Neutral visual stimuli of abstract paintings were presented simultaneously with liked and disliked odours and sounds, with neutral-neutral pairings serving as controls. The results confirm previous findings that the affective evaluation of previously neutral visual stimuli shifts in the direction of contingently presented affective auditory stimuli. In addition, this research shows the presence of conditioning with affective odours having no logical connection with the pictures.

Efficient mining of discriminative molecular fragments

Frequent pattern discovery in structured data is receiving an increasing attention in many application areas of sciences. However, the computational complexity and the large amount of data to be explored often make the sequential algorithms unsuitable. In this context high performance distributed computing becomes a very interesting and promising approach. In this paper we present a parallel formulation of the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The application is characterized by a highly irregular tree-structured computation. No estimation is available for task workloads, which show a power-law distribution in a wide range. The proposed approach allows dynamic resource aggregation and provides fault and latency tolerance. These features make the distributed application suitable for multi-domain heterogeneous environments, such as computational Grids. The distributed application has been evaluated on the well known National Cancer Institute’s HIV-screening dataset.

A double data rate (DDR) architecture for OFDM based wireless consumer devices

The creation of OFDM based Wireless Personal Area Networks (WPANs) has allowed the development of high bit-rate wireless communication devices suitable for streaming High Definition video between consumer products, as demonstrated in Wireless-USB and Wireless-HDMI. However, these devices need high frequency clock rates, particularly for the OFDM, FFT and symbol processing sections resulting in high silicon cost and high electrical power. The high clock rates make hardware prototyping difficult and verification is therefore very important but costly. Acknowledging that electrical power in wireless consumer devices is more critical than the number of implemented logic gates, this paper presents a Double Data Rate (DDR) architecture for implementation inside a OFDM baseband codec in order to reduce the high frequency clock rates by a complete factor of 2. The presented architecture has been implemented and tested for ECMA-368 (Wireless- USB context) resulting in a maximum clock rate of 264MHz instead of the expected 528MHz clock rate existing anywhere on the baseband codec die.

A double data rate (DDR) architecture for OFDM based wireless consumer devices

The creation of OFDM based Wireless Personal Area Networks (WPANs) has allowed high bit-rate wireless communication devices suitable for streaming High Definition video between consumer products as demonstrated in Wireless- USB. However, these devices need high clock rates, particularly for the OFDM sections resulting in high silicon cost and high electrical power. Acknowledging that electrical power in wireless consumer devices is more critical than the number of implemented logic gates, this paper presents a Double Data Rate (DDR) architecture to reduce the OFDM input and output clock rate by a factor of 2. The architecture has been implemented and tested for Wireless-USB (ECMA-368) resulting in a maximum clock of 264MHz instead of 528MHz existing anywhere on the die.

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

Background: Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Results: Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion: The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC.

An approximate Bayesian computation approach to overcome biases that arise when using amplified fragment length polymorphism markers to study population structure

There is great interest in using amplified fragment length polymorphism (AFLP) markers because they are inexpensive and easy to produce. It is, therefore, possible to generate a large number of markers that have a wide coverage of species genotnes. Several statistical methods have been proposed to study the genetic structure using AFLP's but they assume Hardy-Weinberg equilibrium and do not estimate the inbreeding coefficient, F-IS. A Bayesian method has been proposed by Holsinger and colleagues that relaxes these simplifying assumptions but we have identified two sources of bias that can influence estimates based on these markers: (i) the use of a uniform prior on ancestral allele frequencies and (ii) the ascertainment bias of AFLP markers. We present a new Bayesian method that avoids these biases by using an implementation based on the approximate Bayesian computation (ABC) algorithm. This new method estimates population-specific F-IS and F-ST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses. The software is available at our web site (http://www-leca.uif-grenoble.fi-/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias.

When are ant-attractant devices a worthwhile investment? Vicia faba extrafloral nectaries and Lasius niger ants

Most studies aiming to determine the beneficial effect of ants on plants simply consider the effects of the presence or exclusion of ants on plant yield. This approach is often inadequate, however, as ants interact with both non-tended herbivores and tended Homoptera. Moreover, the interaction with these groups of organisms is dependent on ant density, and these functional relationships are likely to be non-linear. A model is presented here that segregates plant herbivores into two categories depending on the sign of their numerical response to ants (myrmecophiles increase with ants, non-tended herbivores decline). The changes in these two components of herbivores with increasing ant density and the resulting implications for ant-plant mutualisms are considered. It emerges that a wide range of ant densities needs to be considered as the interaction sign (mutualism or parasitism) and strength is likely to change with ant density. The model is used to interpret the results of an experimental study that varied levels of Aphis fabae infestation and Lasius niger ant attendance on Vicia faba bean plants. Increasing ant density consistently reduced plant fitness and thus, in this location, the interaction between the ants and the plant can be considered parasitic. In the Vicia faba system, these costs of ants are unlikely to be offset by other beneficial agents (e.g., parasitoids), which also visit extrafloral nectaries.

Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation

We describe and evaluate a new estimator of the effective population size (N-e), a critical parameter in evolutionary and conservation biology. This new "SummStat" N-e. estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N-e. Simulations of a Wright-Fisher population with known N-e show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N-e values. We also address the paucity of information about the relative performance of N-e estimators by comparing the SUMMStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated rising initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE > 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and Ne less than or equal to 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N-e. The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any, potentially informative summary statistic from Population genetic data.