Pool Evolution: A Parallel Pattern for Evolutionary and Symbolic Computing

We introduce a new parallel pattern derived from a specific application domain and show how it turns out to have application beyond its domain of origin. The pool evolution pattern models the parallel evolution of a population subject to mutations and evolving in such a way that a given fitness function is optimized. The pattern has been demonstrated to be suitable for capturing and modeling the parallel patterns underpinning various evolutionary algorithms, as well as other parallel patterns typical of symbolic computation. In this paper we introduce the pattern, we discuss its implementation on modern multi/many core architectures and finally present experimental results obtained with FastFlow and Erlang implementations to assess its feasibility and scalability.

On the Complexity of Universal Leader Election

Electing a leader is a fundamental task in distributed computing. In its implicit version, only the leader must know who is the elected leader. This article focuses on studying the message and time complexity of randomized implicit leader election in synchronous distributed networks. Surprisingly, the most "obvious" complexity bounds have not been proven for randomized algorithms. In particular, the seemingly obvious lower bounds of Ω(m) messages, where m is the number of edges in the network, and Ω(D) time, where D is the network diameter, are nontrivial to show for randomized (Monte Carlo) algorithms. (Recent results, showing that even Ω(n), where n is the number of nodes in the network, is not a lower bound on the messages in complete networks, make the above bounds somewhat less obvious). To the best of our knowledge, these basic lower bounds have not been established even for deterministic algorithms, except for the restricted case of comparison algorithms, where it was also required that nodes may not wake up spontaneously and that D and n were not known. We establish these fundamental lower bounds in this article for the general case, even for randomized Monte Carlo algorithms. Our lower bounds are universal in the sense that they hold for all universal algorithms (namely, algorithms that work for all graphs), apply to every D, m, and n, and hold even if D, m, and n are known, all the nodes wake up simultaneously, and the algorithms can make any use of node's identities. To show that these bounds are tight, we present an O(m) messages algorithm. An O(D) time leader election algorithm is known. A slight adaptation of our lower bound technique gives rise to an Ω(m) message lower bound for randomized broadcast algorithms. 

An interesting fundamental problem is whether both upper bounds (messages and time) can be reached simultaneously in the randomized setting for all graphs. The answer is known to be negative in the deterministic setting. We answer this problem partially by presenting a randomized algorithm that matches both complexities in some cases. This already separates (for some cases) randomized algorithms from deterministic ones. As first steps towards the general case, we present several universal leader election algorithms with bounds that tradeoff messages versus time. We view our results as a step towards understanding the complexity of universal leader election in distributed networks.

Enhancing design space exploration by extending CPU/GPU specifications onto FPGAs

The design cycle for complex special-purpose computing systems is extremely costly and time-consuming. It involves a multiparametric design space exploration for optimization, followed by design verification. Designers of special purpose VLSI implementations often need to explore parameters, such as optimal bitwidth and data representation, through time-consuming Monte Carlo simulations. A prominent example of this simulation-based exploration process is the design of decoders for error correcting systems, such as the Low-Density Parity-Check (LDPC) codes adopted by modern communication standards, which involves thousands of Monte Carlo runs for each design point. Currently, high-performance computing offers a wide set of acceleration options that range from multicore CPUs to Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs). The exploitation of diverse target architectures is typically associated with developing multiple code versions, often using distinct programming paradigms. In this context, we evaluate the concept of retargeting a single OpenCL program to multiple platforms, thereby significantly reducing design time. A single OpenCL-based parallel kernel is used without modifications or code tuning on multicore CPUs, GPUs, and FPGAs. We use SOpenCL (Silicon to OpenCL), a tool that automatically converts OpenCL kernels to RTL in order to introduce FPGAs as a potential platform to efficiently execute simulations coded in OpenCL. We use LDPC decoding simulations as a case study. Experimental results were obtained by testing a variety of regular and irregular LDPC codes that range from short/medium (e.g., 8,000 bit) to long length (e.g., 64,800 bit) DVB-S2 codes. We observe that, depending on the design parameters to be simulated, on the dimension and phase of the design, the GPU or FPGA may suit different purposes more conveniently, thus providing different acceleration factors over conventional multicore CPUs.

Extraordinary solute-stress tolerance contributes to the environmental tenacity of mycobacteria

Mycobacteria are associated with a number of well-characterized diseases, yet we know little about their stress-biology in natural ecosystems. This study focuses on the isolation and characterization of strains from Yellowstone-(YNP) and Glacier-National-Parks (GNP; USA), the majority of those identified were Mycobacterium parascrofulaceum, Mycobacterium avium (YNP) or Mycobacterium gordonae (GNP). Generally, their temperature windows for growth were >60°C; selected isolates grew at super-saturated concentrations of hydrophobic stressors and at levels of osmotic stress and chaotropic activity (up to 13.4 kJkg-1) similar to, or exceeding, those for the xerophilic fungus Aspergillus wentii and solvent-tolerant bacterium Pseudomonas putida. For example, mycobacteria grew down to 0.800 water-activity indicating that they are, with the sole exception of halophiles, more xerotolerant than other bacteria (or any Archaea). Furthermore, the fatty-acid composition of Mycobacterium cells grown over a range of salt concentrations changed less than that of other bacteria, indicating a high level of resilience, regardless of the stress load. Cells of M. parascrofulaceum, M. smegmatis and M. avium resisted the acute, potentially lethal challenges from extremes of pH (<1; >13), and saturated MgCl2-solutions (5 M; 212 kJ kg-1 chaotropicity). Collectively, these findings challenge the paradigm that bacteria have solute tolerances inferior to those of eukaryotes.

Phytoremediation assessment of Gomphrena globosa and Zinnia elegans grown in arsenic-contaminated hydroponic conditions as a safe and feasible alternative to be applied in arsenic-contaminated soils of the Bengal Delta

Several agricultural fields show high contents of arsenic because of irrigation with arsenic- contaminated groundwater. Vegetables accumulate arse- nic in their edible parts when grown in contaminated soils. Polluted vegetables are one of the main sources of arsenic in the food chain, especially for people living in rural arsenic endemic villages of India and Bangladesh. The aim of this study was to assess the feasibility of floriculture in the crop rotation system of arsenic en- demic areas of the Bengal Delta. The effects of different arsenic concentrations (0, 0.5, 1.0, and 2.0 mg As L−1) and types of flowering plant (Gomphrena globosa and Zinnia elegans) on plant growth and arsenic accumula- tion were studied under hydroponic conditions. Total arsenic was quantified using atomic absorption spec- trometer with hydride generation (HG-AAS). Arsenic was mainly accumulated in the roots (72 %), followed by leaves (12 %), stems (10 %), and flowers (<1 %). The flowering plants studied did not show as high phytoremediation capacities as other wild species, suchas ferns. However, they behaved as arsenic tolerant plants and grew and bloomed well, without showing any phytotoxic signs. This study proves that floriculture could be included within the crop rotation system in arsenic-contaminated agricultural soils, in order to im- prove food safety and also food security by increasing farmer’s revenue.

An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response

UNLABELLED: Influenza A viruses counteract the cellular innate immune response at several steps, including blocking RIG I-dependent activation of interferon (IFN) transcription, interferon (IFN)-dependent upregulation of IFN-stimulated genes (ISGs), and the activity of various ISG products; the multifunctional NS1 protein is responsible for most of these activities. To determine the importance of other viral genes in the interplay between the virus and the host IFN response, we characterized populations and selected mutants of wild-type viruses selected by passage through non-IFN-responsive cells. We reasoned that, by allowing replication to occur in the absence of the selection pressure exerted by IFN, the virus could mutate at positions that would normally be restricted and could thus find new optimal sequence solutions. Deep sequencing of selected virus populations and individual virus mutants indicated that nonsynonymous mutations occurred at many phylogenetically conserved positions in nearly all virus genes. Most individual mutants selected for further characterization induced IFN and ISGs and were unable to counteract the effects of exogenous IFN, yet only one contained a mutation in NS1. The relevance of these mutations for the virus phenotype was verified by reverse genetics. Of note, several virus mutants expressing intact NS1 proteins exhibited alterations in the M1/M2 proteins and accumulated large amounts of deleted genomic RNAs but nonetheless replicated to high titers. This suggests that the overproduction of IFN inducers by these viruses can override NS1-mediated IFN modulation. Altogether, the results suggest that influenza viruses replicating in IFN-competent cells have tuned their complete genomes to evade the cellular innate immune system and that serial replication in non-IFN-responsive cells allows the virus to relax from these constraints and find a new genome consensus within its sequence space.

IMPORTANCE: In natural virus infections, the production of interferons leads to an antiviral state in cells that effectively limits virus replication. The interferon response places considerable selection pressure on viruses, and they have evolved a variety of ways to evade it. Although the influenza virus NS1 protein is a powerful interferon antagonist, the contributions of other viral genes to interferon evasion have not been well characterized. Here, we examined the effects of alleviating the selection pressure exerted by interferon by serially passaging influenza viruses in cells unable to respond to interferon. Viruses that grew to high titers had mutations at many normally conserved positions in nearly all genes and were not restricted to the NS1 gene. Our results demonstrate that influenza viruses have fine-tuned their entire genomes to evade the interferon response, and by removing interferon-mediated constraints, viruses can mutate at genome positions normally restricted by the interferon response.

Fasciola hepatica:the effect of the microfilament inhibitor cytochalasin B on the ultrastructure of the adult fluke

The effect of the microfilament inhibitor cytochalasin B (10 and 100 micrograms/ml) on the ultrastructure of adult Fasciola hepatica was determined in vitro by scanning and transmission electron microscopy (SEM, TEM) using both intact flukes and tissue-slice material. SEM revealed that initial swelling of the tegument led to surface blebbing and limited areas of sloughing after 24 h treatment at 100 micrograms/ml. In the tegumental syncytium, basal accumulations of secretory bodies (especially T2s) were evident in the earlier time periods but declined with longer incubations, until few secretory bodies remained in the syncytium overall. Blebbing of the apical plasma membrane and occasional areas of breakdown and sloughing of the tegument were observed over longer periods of treatment at 100 micrograms/ml. In the tegumental cell bodies, the Golgi complexes gradually decreased in size and activity, and few secretory bodies were produced. In the later time periods, the cells assumed abnormal shapes, the cytoplasm shrinking in towards the nucleus. In the vitelline follicles, a random dispersion of shell protein globules was evident within the intermediate-type cells, rather than their being organized into distinct shell globule clusters. Disruption of this process was more severe at the higher concentration of 100 micrograms/ml and again was more evident in tissue-slice material. In the latter, after prolonged (12 h) exposure to cytochalasin B, the intermediate and mature vitelline cells were filled with loosely packed and expanded shell globule clusters, containing few shell protein globules. The mature vitelline cells continued to lay down "yolk" globules and glycogen deposits. Disruption of the network of processes from the nurse cells was evident at the higher concentration of cytochalasin. Spaces began to appear between the vitelline cells and grew larger with progressively longer incubation periods, and the cells themselves assumed abnormal shapes. A number of binucleate stem cells were observed in tissue-slice material at the longest incubation period (12 h).

Robust bimodal person identification using face and speech with limited training data and corruption of both modalities

This paper presents a novel method of audio-visual fusion for person identification where both the speech and facial modalities may be corrupted, and there is a lack of prior knowledge about the corruption. Furthermore, we assume there is a limited amount of training data for each modality (e.g., a short training speech segment and a single training facial image for each person). A new representation and a modified cosine similarity are introduced for combining and comparing bimodal features with limited training data as well as vastly differing data rates and feature sizes. Optimal feature selection and multicondition training are used to reduce the mismatch between training and testing, thereby making the system robust to unknown bimodal corruption. Experiments have been carried out on a bimodal data set created from the SPIDRE and AR databases with variable noise corruption of speech and occlusion in the face images. The new method has demonstrated improved recognition accuracy.

Virtual Thrower Versus Real Goalkeeper: The Influence of Different Visual Conditions on Performance

In order to use virtual reality as a sport analysis tool, we need to be sure that an immersed athlete reacts realistically in a virtual environment. This has been validated for a real handball goalkeeper facing a virtual thrower. However, we currently ignore which visual variables induce a realistic motor behavior of the immersed handball goalkeeper. In this study, we used virtual reality to dissociate the visual information related to the movements of the player from the visual information related to the trajectory of the ball. Thus, the aim is to evaluate the relative influence of these different visual information sources on the goalkeeper's motor behavior. We tested 10 handball goalkeepers who had to predict the final position of the virtual ball in the goal when facing the following: only the throwing action of the attacking player (TA condition), only the resulting ball trajectory (BA condition), and both the throwing action of the attacking player and the resulting ball trajectory (TB condition). Here we show that performance was better in the BA and TB conditions, but contrary to expectations, performance was substantially worse in the TA condition. A significant effect of ball landing zone does, however, suggest that the relative importance between visual information from the player and the ball depends on the targeted zone in the goal. In some cases, body-based cues embedded in the throwing actions may have a minor influence on the ball trajectory and vice versa. Kinematics analysis was then combined with these results to determine why such differences occur depending on the ball landing zone and consequently how it can clarify the role of different sources of visual information on the motor behavior of an athlete immersed in a virtual environment.

Two-Stage Orthogonal Least Squares Methods for Neural Network Construction

A number of neural networks can be formulated as the linear-in-the-parameters models. Training such networks can be transformed to a model selection problem where a compact model is selected from all the candidates using subset selection algorithms. Forward selection methods are popular fast subset selection approaches. However, they may only produce suboptimal models and can be trapped into a local minimum. More recently, a two-stage fast recursive algorithm (TSFRA) combining forward selection and backward model refinement has been proposed to improve the compactness and generalization performance of the model. This paper proposes unified two-stage orthogonal least squares methods instead of the fast recursive-based methods. In contrast to the TSFRA, this paper derives a new simplified relationship between the forward and the backward stages to avoid repetitive computations using the inherent orthogonal properties of the least squares methods. Furthermore, a new term exchanging scheme for backward model refinement is introduced to reduce computational demand. Finally, given the error reduction ratio criterion, effective and efficient forward and backward subset selection procedures are proposed. Extensive examples are presented to demonstrate the improved model compactness constructed by the proposed technique in comparison with some popular methods.

Lead-bismuth eutectic corrosion behaviors of ferritic/martensitic steels in low oxygen concentration environment

In order to investigate the compatibility of candidate structural materials with liquid metals, two kinds of ferritic/martensitic steels were chosen to contact with lead–bismuth eutectic in sealed quartz–glass tubes. The corrosion exposures were for 500 and 3000 h. Results showed that the oxidation layer and carbide dissolution layer on the two steels grew with contact time under oxygen unsaturated condition. Short-term corrosion behavior of a newly developed steel showed better lead–bismuth eutectic corrosion resistance than T91 at 873 K.

Protective role of glycerol against benzene stress: insights from the Pseudomonas putida proteome

Chemical activities of hydrophobic substances can determine the windows of environmental conditions over which microbial systems function and the metabolic inhibition of microorganisms by benzene and other hydrophobes can, paradoxically, be reduced by compounds that protect against cellular water stress (Bhaganna et al. in Microb Biotechnol 3:701-716, 2010; Cray et al. in Curr Opin Biotechnol 33:228-259, 2015a). We hypothesized that this protective effect operates at the macromolecule structure-function level and is facilitated, in part at least, by genome-mediated adaptations. Based on proteome profiling of the soil bacterium Pseudomonas putida, we present evidence that (1) benzene induces a chaotrope-stress response, whereas (2) cells cultured in media supplemented with benzene plus glycerol were protected against chaotrope stress. Chaotrope-stress response proteins, such as those involved in lipid and compatible-solute metabolism and removal of reactive oxygen species, were increased by up to 15-fold in benzene-stressed cells relative to those of control cultures (no benzene added). By contrast, cells grown in the presence of benzene + glycerol, even though the latter grew more slowly, exhibited only a weak chaotrope-stress response. These findings provide evidence to support the hypothesis that hydrophobic substances induce a chaotropicity-mediated water stress, that cells respond via genome-mediated adaptations, and that glycerol protects the cell's macromolecular systems. We discuss the possibility of using compatible solutes to mitigate hydrocarbon-induced stresses in lignocellulosic biofuel fermentations and for industrial and environmental applications.

An effective key generation system using improved channel reciprocity

In physical layer security systems there is a clear need to exploit the radio link characteristics to automatically generate an encryption key between two end points. The success of the key generation depends on the channel reciprocity, which is impacted by the non-simultaneous measurements and the white nature of the noise. In this paper, an OFDM subcarriers' channel responses based key generation system with enhanced channel reciprocity is proposed. By theoretically modelling the OFDM subcarriers' channel responses, the channel reciprocity is modelled and analyzed. A low pass filter is accordingly designed to improve the channel reciprocity by suppressing the noise. This feature is essential in low SNR environments in order to reduce the risk of the failure of the information reconciliation phase during key generation. The simulation results show that the low pass filter improves the channel reciprocity, decreases the key disagreement, and effectively increases the success of the key generation.