Antitrust Challenge to Non-Profit Certification Organizations: Conflicts of Interest and a Practical Rule of Reason Approach to Certification Programs As Industry-Wide Builders of Competition and Efficiency

The paramount antitrust challenge for nonprofit product certification programs is to demonstrate aggressively that such programs strengthen the competitive market system on an industry-wide basis. This affirmative challenge is, however, limited by another urgent antitrust challenge still closer to the courtroom door. This challenge, requiring advance organizational and litigation planning, is to avoid or defeat a possible plaintiff\u27s claim of antitrust abuses by a certification organization whose decision-making participants may be caught in alleged conflicts of interest. These two challenges must be met for certification programs to survive and progress. The only way successfully to meet these antitrust challenges is to make product performance certification programs synonymous with industry-wide competition and productivity and with systems of safeguards against conflicts of interest. Further, this must be proved to the judge and jury. This Commentary will discuss two critical questions that flow from an analytical approach to these two challenges: First, whether a coherent basis exists for viewing nonprofit certification programs as structural elements in the marketplace hierarchy that advance urgent antitrust goals, including increased competition and productivity; and second, whether a distinct duty to safeguard certification organizations against conflicts of interest would, if met, demonstrate that a certification organization under antitrust scrutiny in court should be found to be without conspiratorial intent

An autoencoder compression approach for accelerating large-scale inverse problems

PDE-constrained inverse problems are some of the most challenging and computationally demanding problems in computational science today. Fine meshes that are required to accurately compute the PDE solution introduce an enormous number of parameters and require large scale computing resources such as more processors and more memory to solve such systems in a reasonable time. For inverse problems constrained by time dependent PDEs, the adjoint method that is often employed to efficiently compute gradients and higher order derivatives requires solving a time-reversed, so-called adjoint PDE that depends on the forward PDE solution at each timestep. This necessitates the storage of a high dimensional forward solution vector at every timestep. Such a procedure quickly exhausts the available memory resources. Several approaches that trade additional computation for reduced memory footprint have been proposed to mitigate the memory bottleneck, including checkpointing and compression strategies. In this work, we propose a close-to-ideal scalable compression approach using autoencoders to eliminate the need for checkpointing and substantial memory storage, thereby reducing both the time-to-solution and memory requirements. We compare our approach with checkpointing and an off-the-shelf compression approach on an earth-scale ill-posed seismic inverse problem. The results verify the expected close-to-ideal speedup for both the gradient and Hessian-vector product using the proposed autoencoder compression approach. To highlight the usefulness of the proposed approach, we combine the autoencoder compression with the data-informed active subspace (DIAS) prior to show how the DIAS method can be affordably extended to large scale problems without the need of checkpointing and large memory

Antibacterial Fluoromicas: A Novel Delivery Medium

Antibacterial fluoromicas were prepared by ion-exchanging fluoromicas with different antibacterial agents including various quaternary ammonium compounds, AgNO3, and norfloxacin. Antibacterial activities of the ion-exchanged fluoromicas were determined against Staphylococcus aureus and Escherichia coli. Minimum inhibitory concentration (MIC) and zone of inhibition (ZOI) tests were performed to determine both antibacterial effectiveness and mode of action associated with the fluoromicas. All treated fluoromicas showed excellent antibacterial activities against both types of bacteria. The antibacterial activities of treated fluoromicas were found to be either better than or the same as those of neat antibacterial agents. The repeated antibacterial activity tests demonstrated the extended activity of these systems. © 2007 Elsevier B.V. All rights reserved

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Metagenomic sequence classification is a procedure to assign sequences to their source genomes. It is one of the important steps for metagenomic sequence data analysis. Although many methods exist, classification of high-throughput metagenomic sequence data in a limited time is still a challenge. We present here an ultra-fast metagenomic sequence classification system (MetaBinG) using graphic processing units (GPUs). The accuracy of MetaBinG is comparable to the best existing systems and it can classify a million of 454 reads within five minutes, which is more than 2 orders of magnitude faster than existing systems. MetaBinG is publicly available at http://cbb.sjtu.edu.cn/~ccwei/pub/software/MetaBinG/MetaBinG.php

Robonaut 2 - IVA Experiments On-Board ISS and Development Towards EVA Capability

Robonaut 2 (R2) has completed its fixed base activities on-board the ISS and is scheduled to receive its climbing legs in early 2014. In its continuing line of firsts, the R2 torso finished up its on-orbit activities on its stanchion with the manipulation of space blanket materials and performed multiple tasks under teleoperation control by IVA astronauts. The successful completion of these two IVA experiments is a key step in Robonaut's progression towards an EVA capability. Integration with the legs and climbing inside the ISS will provide another important part of the experience that R2 will need prior to performing tasks on the outside of ISS. In support of these on-orbit activities, R2 has been traversing across handrails in simulated zero-g environments and working with EVA tools and equipment on the ground to determine manipulation strategies for an EVA Robonaut. R2 made significant advances in robotic manipulation of deformable materials in space while working with its softgoods task panel. This panel features quarter turn latches that secure a space blanket to the task panel structure. The space blanket covers two cloth cubes that are attached with Velcro to the structure. R2 was able to open and close the latches, pull back the blanket, and remove the cube underneath. R2 simulated cleaning up an EVA worksite as well, by replacing the cube and reattaching the blanket. In order to interact with the softgoods panel, R2 has both autonomously and with a human in the loop identified and localized these deformable objects. Using stereo color cameras, R2 identified characteristic elements on the softgoods panel then extracted the location and orientation of the object in its field of view using stereo disparity and kinematic transforms. R2 used both vision processing and supervisory control to successfully accomplish this important task. Teleoperation is a key capability for Robonaut's effectiveness as an EVA system. To build proficiency, crewmembers have attempted increasingly difficult tasks using R2 inside the Station. After donning motion capture equipment and a virtual reality visor, Expedition 34/35 flight engineer Tom Marshburn began operations with simple hand movements. Having gained confidence, Marshburn guided R2's arms in a leader-follower exercise with crewmate Chris Cassidy. He was also able to use the hand to grab a tumbling roll of tape, a task only demonstrable in microgravity. Later efforts saw Cassidy handle softgoods through shared control with ground operators, mimicking an activity previously achieved using only autonomy. Robotic climbing through the ISS on handrails requires both precision motion and compliant grasps in order to both position grippers on handrails/seat track and prevent large internal forces. R2 climbs using actively controlled compliance and torque limiting to meet both the precision and softness requirements. During a step, the attached leg is controlled to be strong and stiff in order to maintain precision trajectory tracking. The swing leg is controlled to be stiff but weak to minimize unintentional impact forces while maintaining precision. During a simulated dual limb grasp (as shown in Figure 1), the R2 controller maintains one limb rigid and one limb soft to prevent large internal forces from building up. R2's grippers also use a form of force control to limit grip force while not fully closed on either a handrail or seat track thus limiting unintentional forces on cables/objects that may be present in R2's translational path. The on-board torso R2 safety system relies on a single end-effector velocity limit to prevent potential impact forces from exceeding Station maximum load requirements. R2's mobile configuration required modifications to the velocity limiting safety function due to its large, dynamic inertia. R2's legs maneuver the robot's mass creating configuration dependent, joint-relative inertias. A single all-encompassing velocity limit to cover worst case inertia is prohibitively low. The upgraded R2 control and safety systems solve this problem using momentum limiting, momentum control, and kinetic energy minimization. Momentum and kinetic energy take the robot mass into account relieving low velocity restrictions on low inertia end-effectors while ensuring that the overall mass of R2 is limited from hazardous velocities. The momentum of R2's five safety nodes (each of the four end-effectors and the body) is monitored and compared to a single momentum limit. If any of the five nodes exceeds the safety limit, the motor power is removed and the robot comes to a stop. Momentum control/limiting also provides a simple, reliable method to integrate hand held tools into the safety system by providing the tool mass to the control system thus automatically reducing the allowable velocity of the end-effector with the tool. Work on the ground continues to build the skill set for an EVA Robonaut. Recent experiments (Figure 2) demonstrate how a teleoperator can use R2 to manipulate a tether hook, an important safety precaution on spacewalks. Another task displayed Robonaut's ability to pull back a protective jacket over a hose and search for damage, as well as inspect a quick-disconnect fitting for debris. Demonstrations such as these are indicative of EVA work done on ISS, specifically seen during a series of spacewalks over 2012 and 2013 where astronauts searched for an ammonia leak in one of the external cooling loops. Through experiments both on ISS and on the ground, R2 is evolving and providing the information needed to plan out the upgrades that will make an EVA Robonaut an effective tool. With the addition of legs, R2 will start climbing inside the space station and supply invaluable information on how the climbing strategies and task stabilization techniques must be refined. Ground R2 systems will continue to work with additional EVA tools and equipment in preparation for onboard IVA testing and future EVA applications

A walk into the luxR regulators of actinobacteria : phylogenomic distribution and functional diversity

LuxR regulators are a widely studied group of bacterial helix-turn-helix (HTH) transcription factors involved in the regulation of many genes coding for important traits at an ecological and medical level. This regulatory family is particularly known by their involvement in quorum-sensing (QS) mechanisms, i.e., in the bacterial ability to communicate through the synthesis and binding of molecular signals. However, these studies have been mainly focused on Gram-negative organisms, and the presence of LuxR regulators in the Gram-positive Actinobacteria phylum is still poorly explored. In this manuscript, the presence of LuxR regulators among Actinobacteria was assayed using a domain-based strategy. A total of 991 proteins having one LuxR domain were identified in 53 genome-sequenced actinobacterial species, of which 59% had an additional domain. In most cases (53%) this domain was REC (receiver domain), suggesting that LuxR regulators in Actinobacteria may either function as single transcription factors or as part of two-component systems. The frequency, distribution and evolutionary stability of each of these sub-families of regulators was analyzed and contextualized regarding the ecological niche occupied by each organism. The results show that the presence of extra-domains in the LuxR-regulators was likely driven by a general need to physically uncouple the signal sensing from the signal transduction. Moreover, the total frequency of LuxR regulators was shown to be dependent on genetic, metabolic and ecological variables. Finally, the functional annotation of the LuxR regulators revealed that the bacterial ecological niche has biased the specialization of these proteins. In the case of pathogens, our results suggest that LuxR regulators can be involved in virulence and are therefore promising targets for future studies in the health-related biotechnology field.Fundação para a Ciência e TecnologiaEuropean Regional Development Fund - COMPETE program and FCT - Fundacão para a Ciência e Tecnologia, with the project FCOMP-01-0124-FEDER-022718 (ref FCT Pest-C/SAU/LA0002/2011). MVM was supported by ‘‘Programa Ciência 2007’’ sponsored by POPH QREN Tipologia 4.2 Promoção do Emprego Cientifico program and co-financed by the European Social Fund and Portuguese national funds from the MCTES. CLS was supported by the FCT fellowship SFRH/BPD/62978/2009

The Agaricus bisporus cox1 Gene: The Longest Mitochondrial Gene and the Largest Reservoir of Mitochondrial Group I Introns

In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms. Large introns (up to 5 kbp) are frequent in mitochondrial genomes of plant and fungi but scarce in Metazoa, even if these organisms are grouped with fungi among the Opisthokonts. Mitochondrial introns are classified in two groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism. Most of these mitochondrial group I introns carry a “Homing Endonuclease Gene” (heg) encoding a DNA endonuclease acting in transfer and site-specific integration (“homing”) and allowing intron spreading and gain after lateral transfer even between species from different kingdoms. Opposed to this gain mechanism, is another which implies that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss. The importance of both mechanisms (loss and gain) is matter of debate. Here we report the sequence of the cox1 gene of the button mushroom Agaricus bisporus, the most widely cultivated mushroom in the world. This gene is both the longest mitochondrial gene (29,902 nt) and the largest group I intron reservoir reported to date with 18 group I and 1 group II. An exhaustive analysis of the group I introns available in cox1 genes shows that they are mobile genetic elements whose numerous events of loss and gain by lateral transfer combine to explain their wide and patchy distribution extending over several kingdoms. An overview of intron distribution, together with the high frequency of eroded heg, suggests that they are evolving towards loss. In this landscape of eroded and lost intron sequences, the A. bisporus cox1 gene exhibits a peculiar dynamics of intron keeping and catching, leading to the largest collection of mitochondrial group I introns reported to date in a Eukaryote

Molecular Diversity of Fungal Phylotypes Co-Amplified Alongside Nematodes from Coastal and Deep-Sea Marine Environments

Nematodes and fungi are both ubiquitous in marine environments, yet few studies have investigated relationships between these two groups. Microbial species share many well-documented interactions with both free-living and parasitic nematode species, and limited data from previous studies have suggested ecological associations between fungi and nematodes in benthic marine habitats. This study aimed to further document the taxonomy and distribution of fungal taxa often co-amplified from nematode specimens. A total of 15 fungal 18S rRNA phylotypes were isolated from nematode specimens representing both deep-sea and shallow water habitats; all fungal isolates displayed high pairwise sequence identities with published data in Genbank (99–100%) and unpublished high-throughput 454 environmental datasets (>95%). BLAST matches indicate marine fungal sequences amplified in this study broadly represent taxa within the phyla Ascomycota and Basidiomycota, and several phylotypes showed robust groupings with known taxa in phylogenetic topologies. In addition, some fungal phylotypes appeared to be present in disparate geographic habitats, suggesting cosmopolitan distributions or closely related species complexes in at least some marine fungi. The present study was only able to isolate fungal DNA from a restricted set of nematode taxa; further work is needed to fully investigate the taxonomic scope and function of nematode-fungal interactions

Genome content and phylogenomics reveal both ancestral and lateral evolutionary pathways in plant-pathogenic Streptomyces species

© 2016, American Society for Microbiology. All Rights Reserved. Streptomyces spp. are highly differentiated actinomycetes with large, linear chromosomes that encode an arsenal of biologically active molecules and catabolic enzymes. Members of this genus are well equipped for life in nutrient-limited environments and are common soil saprophytes. Out of the hundreds of species in the genus Streptomyces, a small group has evolved the ability to infect plants. The recent availability of Streptomyces genome sequences, including four genomes of pathogenic species, provided an opportunity to characterize the gene content specific to these pathogens and to study phylogenetic relationships among them. Genome sequencing, comparative genomics, and phylogenetic analysis enabled us to discriminate pathogenic from saprophytic Streptomyces strains; moreover, we calculated that the pathogen-specific genome contains 4,662 orthologs. Phylogenetic reconstruction suggested that Streptomyces scabies and S. ipomoeae share an ancestor but that their biosynthetic clusters encoding the required virulence factor thaxtomin have diverged. In contrast, S. turgidiscabies and S. acidiscabies, two relatively unrelated pathogens, possess highly similar thaxtomin biosynthesis clusters, which suggests that the acquisition of these genes was through lateral gene transfer

A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements, and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.Comment: Documents version 3 of the forma