The imprint of microfibres in southern European deep seas

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Bridging topological and functional information in protein interaction networks by short loops profiling

Protein-protein interaction networks (PPINs) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. In this study we identify fundamental principles of PPIN topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. We compared 30 PPINs with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-validated high-confidence dataset of 622 human protein complexes. We demonstrate that loops are an intrinsic feature of PPINs and that specific cell functions are predominantly performed by loops of different lengths. Topologically, we find that loops are strongly related to the accuracy of PPINs and define a core of interactions with high resilience. The identification of this core and the analysis of loop composition are promising tools to assess PPIN quality and to uncover possible biases from experimental detection methods. More than 96% of loops share at least one biological function, with enrichment of cellular functions related to mRNA metabolic processing and the cell cycle. Our analyses suggest that these motifs can be used in the design of targeted experiments for functional phenotype detection.This research was supported by the Biotechnology and Biological Sciences Research Council (BB/H018409/1 to AP, ACCC and FF, and BB/J016284/1 to NSBT) and by the Leukaemia & Lymphoma Research (to NSBT and FF). SSC is funded by a Leukaemia & Lymphoma Research Gordon Piller PhD Studentship

The effect of intervertebral cartilage on neutral posture and range of motion in the necks of sauropod dinosaurs

The necks of sauropod dinosaurs were a key factor in their evolution. The habitual posture and range of motion of these necks has been controversial, and computer-aided studies have argued for an obligatory sub-horizontal pose. However, such studies are compromised by their failure to take into account the important role of intervertebral cartilage. This cartilage takes very different forms in different animals. Mammals and crocodilians have intervertebral discs, while birds have synovial joints in their necks. The form and thickness of cartilage varies significantly even among closely related taxa. We cannot yet tell whether the neck joints of sauropods more closely resembled those of birds or mammals. Inspection of CT scans showed cartilage:bone ratios of 4.5% for Sauroposeidon and about 20% and 15% for two juvenile Apatosaurus individuals. In extant animals, this ratio varied from 2.59% for the rhea to 24% for a juvenile giraffe. It is not yet possible to disentangle ontogenetic and taxonomic signals, but mammal cartilage is generally three times as thick as that of birds. Our most detailed work, on a turkey, yielded a cartilage:bone ratio of 4.56%. Articular cartilage also added 11% to the length of the turkey's zygapophyseal facets. Simple image manipulation suggests that incorporating 4.56% of neck cartilage into an intervertebral joint of a turkey raises neutral posture by 15°. If this were also true of sauropods, the true neutral pose of the neck would be much higher than has been depicted. An additional 11% of zygapophyseal facet length translates to 11% more range of motion at each joint. More precise quantitative results must await detailed modelling. In summary, including cartilage in our models of sauropod necks shows that they were longer, more elevated and more flexible than previously recognised

Extraordinary absorption of sound in porous lamella-crystals

We present the design of a structured material supporting complete absorption of sound with a broadband response and functional for any direction of incident radiation. The structure which is fabricated out of porous lamellas is arranged into a low-density crystal and backed by a reflecting support. Experimental measurements show that strong all-angle sound absorption with almost zero reflectance takes place for a frequency range exceeding two octaves. We demonstrate that lowering the crystal filling fraction increases the wave interaction time and is responsible for the enhancement of intrinsic material dissipation, making the system more absorptive with less material.The work was supported by the Spanish Ministry of Science and Innovation and European Union FEDER through project FIS2011-29734-C02-01. J.C. gratefully acknowledges financial support from the Danish Council for Independent Research and a Sapere Aude grant (12-134776). V. R. G. gratefully acknowledges financial support from the ''Contratos Post-Doctorales Campus Excelencia Internacional'' UPV CEI-01-11.Christensen, J.; Romero García, V.; Picó Vila, R.; Cebrecos Ruiz, A.; Garcia De Abajo, FJ.; Mortensen, NA.; Willatzen, M.... (2014). Extraordinary absorption of sound in porous lamella-crystals. Scientific Reports. 4(4674). https://doi.org/10.1038/srep04674S44674Mei, J. et al. Dark acoustic metamaterials as super absorbers for low-frequency sound. Nat. Commun. 3, 756 (2012).Leroy, V., Strybulevych, A., Scanlon, M. G. & Page, J. Transmission of ultrasound through a single layer of bubbles. Eur. Phys. J. E 29, 123 (2009).Leroy, V., Bretagne, A., Fink, M. H. W., Tabeling, P. & Tourin, A. Design and characterization of bubble phononic crystals. Appl. Phys. Lett. 95, 171904 (2009).Thomas, E. L. Applied physics: Bubbly but quiet. Nature 462, 990 (2009).Romero-García, V., Sánchez-Pérez, J. V. & Garcia-Raffi, L. M. Tunable wideband bandstop acoustic filter based on two-dimensional multiphysical phenomena periodic systems. J. Appl. Phys. 110, 014904 (2011).Garcia-Chocano, V. M., Cabrera, S. & Sanchez-Dehesa, J. Broadband sound absorption by lattices of microperforated cylindrical shells. Appl. Phys. Lett. 101, 184101 (2012).Kushwaha, M. S., Halevi, P., Dobrzynski, L. & Djafari-Rouhani, B. Acoustic band structure of periodic elastic composites. Phys. Rev. Lett. 71, 2022 (1993).Vasseur, J. O. et al. Experimental and Theoretical Evidence for the Existence of Absolute Acoustic Band Gaps in Two-Dimensional Solid Phononic Crystals. Phys. Rev. Lett. 86, 3012 (2001).Liu, Z. et al. Locally Resonant Sonic Materials. Science 289, 1734 (2000).Christensen, J., Martin-Moreno, L. & Garcia-Vidal, F. J. All-angle blockage of sound by an acoustic double-fishnet metamaterial. Appl. Phys. Lett. 97, 134106 (2010).Botten, L. C., Craig, M. S., McPhedran, R. C., Adams, J. L. & Andrewartha, J. R. The finitely conducting lamellar diffraction grating. Optica Acta 28, 1087 (1981).McPhedran, R. C., Botten, L. C., Craif, M. S., Neviere, M. & Maystre, D. Lossy lamellar gratings in the quasistatic limit. Optica Acta 29, 289 (1982).Kravets, V. G., Schedin, F. & Grigorenko, A. N. Plasmonic blackbody: Almost complete absorption of light in nanostructured metallic coatings. Phys. Rev. B 78, 205405 (2008).Sondergaard, T. et al. Plasmonic black gold by adiabatic nanofocusing and absorption of light in ultra-sharp convex grooves. Nat. Commun. 3, 969 (2012).Clapham, P. B. & Hurtley, M. C. Reduction of Lens Reflexion by the Moth Eye Principle. Nature Vol. 244, 281 (1973).Garcia-Vidal, F. J., Pitarke, J. M. & Pendry, J. B. Effective Medium Theory of the Optical Properties of Aligned Carbon Nanotubes. Phys. Rev. Lett. 78, 4289 (1997).Yang, Z., Ci, L., Bur, J. A., Lin, S. & Ajayan, P. M. Experimental Observation of an Extremely Dark Material Made By a Low-Density Nanotube Array. Nano Lett. 8, 446 (2008).Garcia-Vidal, F. J. Metamaterials: Towards the dark side. Nat. Photonics 2, 215 (2008).Mizunoa, K. et al. A black body absorber from vertically aligned single-walled carbon nanotubes. Proc. Natl. Acad. Sci. USA 106, 6044 (2009).Lidorkis, E. & Ferrari, A. C. Photonics with Multiwall Carbon Nanotube Arrays. ACS Nano 3, 1238 (2009).Beenakker, C. W. J. & Brouwer, P. W. Distribution of the reflection eigenvalues of a weakly absorbing chaotic cavity. Physica E 9, 463 (2001).Lafarge, D., Lemarinier, P., Allard, J. F. & Tarnow, V. Dynamic compressibility of air in porous structures at audible frequencies. J. Acoust. Soc. Am. 102, 1995 (1997), With the macroscopic parameters: ϕ = 0.94, α∞ = 1, σ = 20000 Nm−4s and Λ = Λ′ = 0.41 μm.García de Abajo, F. J. Colloquium: Light scattering by particle and hole arrays. Rev. Mod. Phys. 79, 1267–1290 (2007)

Holographic c-theorems in arbitrary dimensions

We re-examine holographic versions of the c-theorem and entanglement entropy in the context of higher curvature gravity and the AdS/CFT correspondence. We select the gravity theories by tuning the gravitational couplings to eliminate non-unitary operators in the boundary theory and demonstrate that all of these theories obey a holographic c-theorem. In cases where the dual CFT is even-dimensional, we show that the quantity that flows is the central charge associated with the A-type trace anomaly. Here, unlike in conventional holographic constructions with Einstein gravity, we are able to distinguish this quantity from other central charges or the leading coefficient in the entropy density of a thermal bath. In general, we are also able to identify this quantity with the coefficient of a universal contribution to the entanglement entropy in a particular construction. Our results suggest that these coefficients appearing in entanglement entropy play the role of central charges in odd-dimensional CFT's. We conjecture a new c-theorem on the space of odd-dimensional field theories, which extends Cardy's proposal for even dimensions. Beyond holography, we were able to show that for any even-dimensional CFT, the universal coefficient appearing the entanglement entropy which we calculate is precisely the A-type central charge.Comment: 62 pages, 4 figures, few typo's correcte

Empirical Installation of Linear Algebra Shared-Memory Subroutines for Auto-Tuning

The final publication is available at Springer via http://dx.doi.org/10.1007/s10766-013-0249-6The introduction of auto-tuning techniques in linear algebra shared-memory routines is analyzed. Information obtained in the installation of the routines is used at running time to take some decisions to reduce the total execution time. The study is carried out with routines at different levels (matrix multiplication, LU and Cholesky factorizations and linear systems symmetric or general routines) and with calls to routines in the LAPACK and PLASMA libraries with multithread implementations. Medium NUMA and large cc-NUMA systems are used in the experiments. This variety of routines, libraries and systems allows us to obtain general conclusions about the methodology to use for linear algebra shared-memory routines auto-tuning. Satisfactory execution times are obtained with the proposed methodology.Partially supported by Fundacion Seneca, Consejeria de Educacion de la Region de Murcia, 08763/PI/08, PROMETEO/2009/013 from Generalitat Valenciana, the Spanish Ministry of Education and Science through TIN2012-38341-C04-03, and the High-Performance Computing Network on Parallel Heterogeneus Architectures (CAPAP-H). The authors gratefully acknowledge the computer resources and assistance provided by the Supercomputing Centre of the Scientific Park Foundation of Murcia and by the Centre de Supercomputacio de Catalunya.Cámara, J.; Cuenca, J.; Giménez, D.; García, LP.; Vidal Maciá, AM. (2014). Empirical Installation of Linear Algebra Shared-Memory Subroutines for Auto-Tuning. 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Holographic Geometry of Entanglement Renormalization in Quantum Field Theories

We study a conjectured connection between the AdS/CFT and a real-space quantum renormalization group scheme, the multi-scale entanglement renormalization ansatz (MERA). By making a close contact with the holographic formula of the entanglement entropy, we propose a general definition of the metric in the MERA in the extra holographic direction, which is formulated purely in terms of quantum field theoretical data. Using the continuum version of the MERA (cMERA), we calculate this emergent holographic metric explicitly for free scalar boson and free fermions theories, and check that the metric so computed has the properties expected from AdS/CFT. We also discuss the cMERA in a time-dependent background induced by quantum quench and estimate its corresponding metric.Comment: 42pages, 9figures, reference added, minor chang

Holographic phase diagram of quark-gluon plasma formed in heavy-ions collisions

The phase diagram of quark gluon plasma (QGP) formed at a very early stage just after the heavy ion collision is obtained by using a holographic dual model for the heavy ion collision. In this dual model colliding ions are described by the charged shock gravitational waves. Points on the phase diagram correspond to the QGP or hadronic matter with given temperatures and chemical potentials. The phase of QGP in dual terms is related to the case when the collision of shock waves leads to formation of trapped surface. Hadronic matter and other confined states correspond to the absence of trapped surface after collision. Multiplicity of the ion collision process is estimated in the dual language as area of the trapped surface. We show that a non-zero chemical potential reduces the multiplicity. To plot the phase diagram we use two different dual models of colliding ions, the point and the wall shock waves, and find qualitative agreement of the results.Comment: 33 pages, 14 figures, typos correcte

The deep sea is a major sink for microplastic debris

Marine debris, mostly consisting of plastic, is a global problem, negatively impacting wildlife, tourism and shipping. However, despite the durability of plastic, and the exponential increase in its production, monitoring data show limited evidence of concomitant increasing concentrations in marine habitats. There appears to be a considerable proportion of the manufactured plastic that is unaccounted for in surveys tracking the fate of environmental plastics. Even the discovery of widespread accumulation of microscopic fragments (microplastics) in oceanic gyres and shallow water sediments is unable to explain the missing fraction. Here, we show that deep-sea sediments are a likely sink for microplastics. Microplastic, in the form of fibres, was up to four orders of magnitude more abundant (per unit volume) in deep-sea sediments from the Atlantic Ocean, Mediterranean Sea and Indian Ocean than in contaminated sea-surface waters. Our results show evidence for a large and hitherto unknown repository of microplastics. The dominance of microfibres points to a previously underreported and unsampled plastic fraction. Given the vastness of the deep sea and the prevalence of microplastics at all sites we investigated, the deep-sea floor appears to provide an answer to the question— where is all the plastic? </jats:p