Phage inducible islands in the gram-positive cocci

The SaPIs are a cohesive subfamily of extremely common phage-inducible chromosomal islands (PICIs) that reside quiescently at specific att sites in the staphylococcal chromosome and are induced by helper phages to excise and replicate. They are usually packaged in small capsids composed of phage virion proteins, giving rise to very high transfer frequencies, which they enhance by interfering with helper phage reproduction. As the SaPIs represent a highly successful biological strategy, with many natural Staphylococcus aureus strains containing two or more, we assumed that similar elements would be widespread in the Gram-positive cocci. On the basis of resemblance to the paradigmatic SaPI genome, we have readily identified large cohesive families of similar elements in the lactococci and pneumococci/streptococci plus a few such elements in Enterococcus faecalis. Based on extensive ortholog analyses, we found that the PICI elements in the four different genera all represent distinct but parallel lineages, suggesting that they represent convergent evolution towards a highly successful lifestyle. We have characterized in depth the enterococcal element, EfCIV583, and have shown that it very closely resembles the SaPIs in functionality as well as in genome organization, setting the stage for expansion of the study of elements of this type. In summary, our findings greatly broaden the PICI family to include elements from at least three genera of cocci

Force Control Improvement in Collaborative Robots through Theory Analysis and Experimental Endorsement

[EN] Due to the elasticity of their joints, collaborative robots are seldom used in applications with force control. Besides, the industrial robot controllers are closed and do not allow the user to access the motor torques and other parameters, hindering the possibility of carrying out a customized control. A good alternative to achieve a custom force control is sending the output of the force regulator to the robot controller through motion commands (inner/outer loop control). There are different types of motion commands (e.g., position or velocity). They may be implemented in different ways (Jacobian inverse vs. Jacobian transpose), but this information is usually not available for the user. This article is dedicated to the analysis of the effect of different inner loops and their combination with several external controllers. Two of the most determinant factors found are the type of the inner loop and the stiffness matrix. The theoretical deductions have been experimentally verified on a collaborative robot UR3, allowing us to choose the best behaviour in a polishing operation according to pre-established criteria.The authors are grateful for the financial support of the Spanish Ministry of Economy and European Union, grant DPI2016-81002-R (AEI/FEDER, UE), to the research work here published. Rodrigo Perez-Ubeda is grateful to the Ph.D. Grant CONICYT PFCHA/DOCTORADO BECAS CHILE/2017-72180157.Pérez-Ubeda, R.; Zotovic Stanisic, R.; Gutiérrez, SC. (2020). Force Control Improvement in Collaborative Robots through Theory Analysis and Experimental Endorsement. Applied Sciences. 10(12):1-24. https://doi.org/10.3390/app10124329S1241012Top Trends Robotics 2020—International Federation of Robotics https://ifr.org/ifr-press-releases/news/top-trends-robotics-2020Gaz, C., Magrini, E., & De Luca, A. (2018). A model-based residual approach for human-robot collaboration during manual polishing operations. Mechatronics, 55, 234-247. doi:10.1016/j.mechatronics.2018.02.014Iglesias, I., Sebastián, M. A., & Ares, J. E. (2015). Overview of the State of Robotic Machining: Current Situation and Future Potential. Procedia Engineering, 132, 911-917. doi:10.1016/j.proeng.2015.12.577Perez-Ubeda, R., Gutierrez, S. C., Zotovic, R., & Lluch-Cerezo, J. (2019). Study of the application of a collaborative robot for machining tasks. Procedia Manufacturing, 41, 867-874. doi:10.1016/j.promfg.2019.10.009Spong, M. W. (1989). On the force control problem for flexible joint manipulators. IEEE Transactions on Automatic Control, 34(1), 107-111. doi:10.1109/9.8661Ren, T., Dong, Y., Wu, D., & Chen, K. (2019). Impedance control of collaborative robots based on joint torque servo with active disturbance rejection. Industrial Robot: the international journal of robotics research and application, 46(4), 518-528. doi:10.1108/ir-06-2018-0130Ajoudani, A., Tsagarakis, N. G., & Bicchi, A. (2017). Choosing Poses for Force and Stiffness Control. IEEE Transactions on Robotics, 33(6), 1483-1490. doi:10.1109/tro.2017.2708087Magrini, E., & De Luca, A. (2016). Hybrid force/velocity control for physical human-robot collaboration tasks. 2016 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS). doi:10.1109/iros.2016.7759151Ahmad, S. (1993). Constrained motion (force/position) control of flexible joint robots. IEEE Transactions on Systems, Man, and Cybernetics, 23(2), 374-381. doi:10.1109/21.229451Calanca, A., & Fiorini, P. (2018). Understanding Environment-Adaptive Force Control of Series Elastic Actuators. IEEE/ASME Transactions on Mechatronics, 23(1), 413-423. doi:10.1109/tmech.2018.2790350Oh, S., & Kong, K. (2017). High-Precision Robust Force Control of a Series Elastic Actuator. IEEE/ASME Transactions on Mechatronics, 22(1), 71-80. doi:10.1109/tmech.2016.2614503Yin, H., Li, S., & Wang, H. (2016). Sliding mode position/force control for motion synchronization of a flexible-joint manipulator system with time delay. 2016 35th Chinese Control Conference (CCC). doi:10.1109/chicc.2016.7554329Ma, Z., Hong, G.-S., Ang, M. H., Poo, A.-N., & Lin, W. (2018). A Force Control Method with Positive Feedback for Industrial Finishing Applications. 2018 IEEE/ASME International Conference on Advanced Intelligent Mechatronics (AIM). doi:10.1109/aim.2018.8452689Huang, L., Ge, S. S., & Lee, T. H. (2006). Position/force control of uncertain constrained flexible joint robots. Mechatronics, 16(2), 111-120. doi:10.1016/j.mechatronics.2005.10.002Chiaverini, S., Siciliano, B., & Villani, L. (1999). A survey of robot interaction control schemes with experimental comparison. IEEE/ASME Transactions on Mechatronics, 4(3), 273-285. doi:10.1109/3516.789685Winkler, A., & Suchy, J. (2016). Explicit and implicit force control of an industrial manipulator — An experimental summary. 2016 21st International Conference on Methods and Models in Automation and Robotics (MMAR). doi:10.1109/mmar.2016.7575081Neranon, P., & Bicker, R. (2016). Force/position control of a robot manipulator for human-robot interaction. Thermal Science, 20(suppl. 2), 537-548. doi:10.2298/tsci151005036nChen, S., Zhang, T., & Zou, Y. (2017). Fuzzy-Sliding Mode Force Control Research on Robotic Machining. Journal of Robotics, 2017, 1-8. doi:10.1155/2017/8128479Lin, H.-I., & Dubey, V. (2018). Design of an Adaptive Force Controlled Robotic Polishing System Using Adaptive Fuzzy-PID. Advances in Intelligent Systems and Computing, 825-836. doi:10.1007/978-3-030-01370-7_64Perez-Vidal, C., Gracia, L., Sanchez-Caballero, S., Solanes, J. E., Saccon, A., & Tornero, J. (2019). Design of a polishing tool for collaborative robotics using minimum viable product approach. International Journal of Computer Integrated Manufacturing, 32(9), 848-857. doi:10.1080/0951192x.2019.1637026Chen, F., Zhao, H., Li, D., Chen, L., Tan, C., & Ding, H. (2019). Contact force control and vibration suppression in robotic polishing with a smart end effector. Robotics and Computer-Integrated Manufacturing, 57, 391-403. doi:10.1016/j.rcim.2018.12.019Mohammad, A. E. K., Hong, J., & Wang, D. (2018). Design of a force-controlled end-effector with low-inertia effect for robotic polishing using macro-mini robot approach. Robotics and Computer-Integrated Manufacturing, 49, 54-65. doi:10.1016/j.rcim.2017.05.011Xiao, C., Wang, Q., Zhou, X., Xu, Z., Lao, X., & Chen, Y. (2019). Hybrid Force/Position Control Strategy for Electromagnetic based Robotic Polishing Systems. 2019 Chinese Control Conference (CCC). doi:10.23919/chicc.2019.8865183Li, J., Zhang, T., Liu, X., Guan, Y., & Wang, D. (2018). A Survey of Robotic Polishing. 2018 IEEE International Conference on Robotics and Biomimetics (ROBIO). doi:10.1109/robio.2018.8664890Zollo, L., Siciliano, B., De Luca, A., Guglielmelli, E., & Dario, P. (2004). Compliance Control for an Anthropomorphic Robot with Elastic Joints: Theory and Experiments. Journal of Dynamic Systems, Measurement, and Control, 127(3), 321-328. doi:10.1115/1.1978911Han, D., Duan, X., Li, M., Cui, T., Ma, A., & Ma, X. (2017). Interaction Control for Manipulator with compliant end-effector based on hybrid position-force control. 2017 IEEE International Conference on Mechatronics and Automation (ICMA). doi:10.1109/icma.2017.8015929Schindlbeck, C., & Haddadin, S. (2015). Unified passivity-based Cartesian force/impedance control for rigid and flexible joint robots via task-energy tanks. 2015 IEEE International Conference on Robotics and Automation (ICRA). doi:10.1109/icra.2015.7139036Zotovic Stanisic, R., & Valera Fernández, Á. (2009). Simultaneous velocity, impact and force control. Robotica, 27(7), 1039-1048. doi:10.1017/s0263574709005451Volpe, R., & Khosla, P. (1993). A theoretical and experimental investigation of explicit force control strategies for manipulators. IEEE Transactions on Automatic Control, 38(11), 1634-1650. doi:10.1109/9.262033Zeng, G., & Hemami, A. (1997). An overview of robot force control. Robotica, 15(5), 473-482. doi:10.1017/s026357479700057xSalisbury, J. (1980). Active stiffness control of a manipulator in cartesian coordinates. 1980 19th IEEE Conference on Decision and Control including the Symposium on Adaptive Processes. doi:10.1109/cdc.1980.272026Chen, S.-F., & Kao, I. (2000). Conservative Congruence Transformation for Joint and Cartesian Stiffness Matrices of Robotic Hands and Fingers. The International Journal of Robotics Research, 19(9), 835-847. doi:10.1177/02783640022067201Institute of Robotics and Mechatronics DLR Light Weight Robot III https://www.dlr.de/rm/en/desktopdefault.aspx/tabid-12464/#gallery/2916

Behavioural Study of the Force Control Loop Used in a Collaborative Robot for Sanding Materials

[EN] The rise of collaborative robots urges the consideration of them for different industrial tasks such as sanding. In this context, the purpose of this article is to demonstrate the feasibility of using collaborative robots in processing operations, such as orbital sanding. For the demonstration, the tools and working conditions have been adjusted to the capacity of the robot. Materials with different characteristics have been selected, such as aluminium, steel, brass, wood, and plastic. An inner/outer control loop strategy has been used, complementing the robot¿s motion control with an outer force control loop. After carrying out an explanatory design of experiments, it was observed that it is possible to perform the operation in all materials, without destabilising the control, with a mean force error of 0.32%. Compared with industrial robots, collaborative ones can perform the same sanding task with similar results. An important outcome is that unlike what might be thought, an increase in the applied force does not guarantee a better finish. In fact, an increase in the feed rate does not produce significant variation in the finish¿less than 0.02 m; therefore, the process is in a ¿saturation state¿ and it is possible to increase the feed rate to increase productivity.Rodrigo Perez-Ubeda is grateful to the Ph.D. Grant CONICYT PFCHA/Doctorado Becas Chile/2017-72180157 and the University of Antofagasta, Chile.Pérez Ubeda, R.; Gutiérrez, SC.; Zotovic Stanisic, R.; Perles, A. (2020). Behavioural Study of the Force Control Loop Used in a Collaborative Robot for Sanding Materials. Materials. 14(1):1-19. https://doi.org/10.3390/ma14010067S11914

Influence of Maturity and Vineyard Location on Free and Bound Aroma Compounds of Grapes from the País Cultivar

Some of the volatile compounds present in grapes give wine is its unique and genuine characteristics.  “Terroir” and berry maturity are considered to be the main influences on the expression of these characteristics. This work was undertaken to establish the specific characteristics that define Vitis vinifera cv. País, based on its aromatic profile and free and bound compounds (glycosides), and to assess the effects of location and maturity. Free and bound volatile compounds presented significant differences in the three locations studied. The total amount of free alcohols, acids and ketones depended on the location. During ripening, the amount of aroma precursors increased in all chemical groups in every location studied, and they were found mainly in the skins. With reference to free volatile compounds, it was found that cis-2-hexenol could be a good candidate to assess maturity, and that terpene content seemed to be strongly related to the vineyard location and cultivar conditions. Also, data analysis showed that the free aroma profile seemed to be influenced more by the maturity of the grapes and the bound aroma fraction more by the location

Sequence determinants for DNA packaging specificity in the S. aureus pathogenicity island SaPI1

The SaPIs and their relatives are a family of genomic islands that exploit helper phages for high frequency horizontal transfer. One of the mechanisms used by SaPIs to accomplish this molecular piracy is the redirection of the helper phage DNA packaging machinery. SaPIs encode a small terminase subunit that can be substituted for that of the phage. In this study we have determined the initial packaging cleavage sites for helper phage 80α, which uses the phage-encoded small terminase subunit, and for SaPI1, which uses the SaPI-encoded small terminase subunit. We have identified a 19 nt SaPI1 sequence that is necessary and sufficient to allow high frequency 80α transduction of a plasmid by a terminase carrying the SaPI1-encoded small subunit. We also show that the hybrid enzyme with the SaPI1 small terminase subunit is capable of generalized transduction.This work was performed in part under FDA's Medical Countermeasures Initiative, Contract #HHSF2232010000521 and NIH 1R56 AI081837 (to GEC). JCB was supported by the Portuguese Institute Fundacao para a Ciencia e Tecnologia (FCT), PhD Fellowship SFRH/BD/66250/2009. E.K.R. was supported by the National Academies National Research Council; his contribution to this study was carried out at NICHHD, NIH, Bethesda, MD, in the laboratory of the late Robert A. Weisberg. Plasmid pCN51 (in strain NRS613) and strain RN4282 (NRS145) were obtained through the Network of Antimicrobial Resistance in Staphylococcus aureus (NARSA) program supported under NIAID/NIFI contract #HHSN272200700055C

Compounds from multilayer plastic bags cause reproductive failures in artificial insemination

High levels of reproductive failure were detected in some Spanish sow farms in the Spring of 2010. Regular returns to estrus and variable reductions in litter size were observed. The problem started suddenly and did not appear to be related to the quality of the ejaculates, disease, alterations of body condition or any other apparent reasons. Subsequent studies determined that the problem was the origin of the plastic bags used for semen storage. Chemical analysis of the suspicious bags identified unexpected compounds such as BADGE, a cyclic lactone and an unknown phthalate that leached into the semen at concentrations of 0.2 to 2.5 mg/L. Spermatozoa preserved in these bags passed all of the routine quality control tests, and no differences were observed between storage in the control and suspicious bags (p . 0.05). In vitro fecundation tests and endocrine profiler panel analysis (EPP) did not show any alterations, whereas the in vivo tests confirmed the described failure. This is the first described relationship between reproductive failure and toxic compounds released from plastic bags

LEGUS Discovery of a Light Echo Around Supernova 2012aw

We have discovered a luminous light echo around the normal Type II-Plateau Supernova (SN) 2012aw in Messier 95 (M95; NGC 3351), detected in images obtained approximately two years after explosion with the Wide Field Channel 3 on-board the Hubble Space Telescope (HST) by the Legacy ExtraGalactic Ultraviolet Survey (LEGUS). The multi-band observations span from the near-ultraviolet through the optical (F275W, F336W, F438W, F555W, and F814W). The apparent brightness of the echo at the time was ~21--22 mag in all of these bands. The echo appears circular, although less obviously as a ring, with an inhomogeneous surface brightness, in particular, a prominent enhanced brightness to the southeast. The SN itself was still detectable, particularly in the redder bands. We are able to model the light echo as the time-integrated SN light scattered off of diffuse interstellar dust in the SN environment. We have assumed that this dust is analogous to that in the Milky Way with R_V=3.1. The SN light curves that we consider also include models of the unobserved early burst of light from the SN shock breakout. Our analysis of the echo suggests that the distance from the SN to the scattering dust elements along the echo is ~45 pc. The implied visual extinction for the echo-producing dust is consistent with estimates made previously from the SN itself. Finally, our estimate of the SN brightness in F814W is fainter than that measured for the red supergiant star at the precise SN location in pre-SN images, possibly indicating that the star has vanished and confirming it as the likely SN progenitor.Comment: 10 pages, 9 figures, to appear in the Astrophysical Journa

Low-density colloid centrifugation removes bacteria from boar semen doses after spiking with selected species

Single-layer centrifugation (SLC) with a low-density colloid is an efficient method for removing contaminating microorganisms from boar semen while recovering most spermatozoa from the original sample. This study tested the performance of this technique, using 50-ml tubes, by spiking commercial semen doses prepared without antibiotics with selected bacterial species followed by storage at 17 degrees C. The doses were spiked up to 102/ml CFU (colony forming units) of the bacteria Burkholderia ambifaria, Pseudomonas aeruginosa, and Staphylococcus sim-ulans. The semen was processed by SLC (15 ml of sample and 15 ml of colloid) with the colloid Porcicoll at 20% (P20) and 30% (P30), with a spiked control (CTL) and an unspiked control (CTL0), analyzing microbiology and sperm quality on days 0, 3 and 7. SLC completely removed B. ambifaria and S. simulans, considerably reducing P. aeruginosa and overall contamination (especially P30, similar to 104 CFU/ml of total contamination on day 7, median). Sperm viability was lower in P20 and P30 samples at day 0, with higher cytoplasmic ROS. Still, results were similar in all groups on day 3 and reversed on day 7, indicating a protective effect of SLC (possibly directly by removal of damaged sperm and indirectly because of lower bacterial contamination). Sperm chromatin was affected by the treatment (lower DNA fragmentation and chromatin decondensation) and storage (higher overall condensation on day 7 as per chromomycin A3 and monobromobimane staining). In conclusion, SLC with low-density colloids can remove most bacteria in a controlled contamination design while potentially improving sperm quality and long-term storage at practical temperatures

The properties, origin and evolution of stellar clusters in galaxy simulations and observations

We investigate the properties and evolution of star particles in two simulations of isolated spiral galaxies, and two galaxies from cosmological simulations. Unlike previous numerical work, where typically each star particle represents one ‘cluster’, for the isolated galaxies we are able to model features we term ‘clusters’ with groups of particles. We compute the spatial distribution of stars with different ages, and cluster mass distributions, comparing our findings with observations including the recent LEGUS survey. We find that spiral structure tends to be present in older (100s Myrs) stars and clusters in the simulations compared to the observations. This likely reflects differences in the numbers of stars or clusters, the strength of spiral arms, and whether the clusters are allowed to evolve. Where we model clusters with multiple particles, we are able to study their evolution. The evolution of simulated clusters tends to follow that of their natal gas clouds. Massive, dense, long-lived clouds host massive clusters, whilst short-lived clouds host smaller clusters which readily disperse. Most clusters appear to disperse fairly quickly, in basic agreement with observational findings. We note that embedded clusters may be less inclined to disperse in simulations in a galactic environment with continuous accretion of gas onto the clouds than isolated clouds and correspondingly, massive young clusters which are no longer associated with gas tend not to occur in the simulations. Caveats of our models include that the cluster densities are lower than realistic clusters, and the simplistic implementation of stellar feedback