The group structure of non-Abelian NS-NS transformations

We study the transformations of the worldvolume fields of a system of multiple coinciding D-branes under gauge transformations of the supergravity Kalb-Ramond field. We find that the pure gauge part of these NS-NS transformations can be written as a U(N) symmetry of the underlying Yang-Mills group, but that in general the full NS-NS variations get mixed up non-trivially with the U(N). We compute the commutation relations and the Jacobi identities of the bigger group formed by the NS-NS and U(N) transformations.Comment: Latex, 11 pages. v2: Typos corrected; version to appear in JHEP

Formation, evolution and multiplicity of brown dwarfs and giant exoplanets

This proceeding summarises the talk of the awardee of the Spanish Astronomical Society award to the the best Spanish thesis in Astronomy and Astrophysics in the two-year period 2006-2007. The thesis required a tremendous observational effort and covered many different topics related to brown dwarfs and exoplanets, such as the study of the mass function in the substellar domain of the young sigma Orionis cluster down to a few Jupiter masses, the relation between the cluster stellar and substellar populations, the accretion discs in cluster brown dwarfs, the frequency of very low-mass companions to nearby young stars at intermediate and wide separations, or the detectability of Earth-like planets in habitable zones around ultracool (L- and T-type) dwarfs in the solar neighbourhood.Comment: "Highlights of Spanish Astrophysics V", Proceedings of the VIII Scientific Meeting of the Spanish Astronomical Society (SEA) held in Santander, 7-11 July, 2008. Edited by J. Gorgas, L. J. Goicoechea, J. I. Gonzalez-Serrano, J. M. Diego. Invited oral contribution to plenary sessio

Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape

BIO2014-57291-R and SAF2017-88908-R from the Spanish Ministry of Economy and Competitivenessgrant PI15/00854 from the FIS“Plataforma de Recursos Biomoleculares y Bioinformáticos” PT17/0009/0006 from the ISCIII, cofunded with European Regional Development FundsFP7-PEOPLE-2012-ITN MLPM2012EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERAT

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome

Spanish Ministry of Economy and Competitiveness grant BIO2014–57291-RSpanish Ministry of Economy and Competitiveness grant SAF2017–88908-R“Plataforma de Recursos Biomoleculares y Bioinformáticos” PT13/0001/0007EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 676559)EU FP7-People ITN Marie Curie Project (ref 316861)

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

This work is supported by grants BIO2014- 57291-R from the Spanish Ministry of Economy and Competitiveness and “Plataforma de Recursos Biomoleculares y Bioinformáticos” PT13/0001/0007 from the ISCIII, both co-funded with European Regional Development Funds (ERDF); PROMETEOII/2014/025 from the Generalitat Valenciana (GVA-FEDER); Fundació la Marató TV3 (ref. 20133134); and EU H2020- INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 676559) and EU FP7-People ITN Marie Curie Project (ref 316861)

Towards Erlang Verification by Term Rewriting

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-14125-1_7This paper presents a transformational approach to the verification of Erlang programs. We define a stepwise transformation from (first-order) Erlang programs to (non-deterministic) term rewrite systems that compute an overapproximation of the original Erlang program. In this way, existing techniques for term rewriting become available. Furthermore, one can use narrowing as a symbolic execution extension of rewriting in order to design a verification technique. We illustrate our approach with some examples, including a deadlock analysis of a simple Erlang program.Vidal Oriola, GF. (2013). Towards Erlang Verification by Term Rewriting. En Logic-Based Program Synthesis and Transformation. Springer. 109-126. doi:10.1007/978-3-319-14125-1_7S109126Albert, E., Arenas, P., Gómez-Zamalloa, M.: Symbolic Execution of Concurrent Objects in CLP. In: Russo, C., Zhou, N.-F. (eds.) PADL 2012. LNCS, vol. 7149, pp. 123–137. Springer, Heidelberg (2012)Albert, E., Vidal, G.: The narrowing-driven approach to functional logic program specialization. New Generation Computing 20(1), 3–26 (2002)Joe, A., Robert, V., Williams, M.: Concurrent programming in ERLANG. Prentice Hall (1993)Arts, T., Earle, C.B., Derrick, J.: Development of a verified Erlang program for resource locking. STTT 5(2–3), 205–220 (2004)Baader, F., Nipkow, T.: Term Rewriting and All That. Cambridge University Press (1998)Caballero, R., Martin-Martin, E., Riesco, A., Tamarit, S.: A Declarative Debugger for Sequential Erlang Programs. In: Veanes, M., Viganò, L. (eds.) TAP 2013. LNCS, vol. 7942, pp. 96–114. Springer, Heidelberg (2013)Claessen, K., Svensson, H.: A semantics for distributed Erlang. In: Sagonas, K.F., Armstrong, J. (eds.). In: Proc. of the 2005 ACM SIGPLAN Workshop on Erlang, pp. 78–87. ACM (2005)Earle, C.B.: Symbolic program execution using the Erlang verification tool. In: Alpuente, M. (eds.) Proc. of the 9th International Workshop on Functional and Logic Programming (WFLP 2000), pp. 42–55 (2000)Felleisen, M., Friedman, D.P., Kohlbecker, E.E., Duba, B.F.: A syntactic theory of sequential control. Theor. Comput. Sci. 52, 205–237 (1987)Fredlund, L.-A., Svensson, H.: McErlang: a model checker for a distributed functional programming language. In: Hinze, R., Ramsey, N. (eds). In: Proc. of ICFP 2007, pp. 125–136. ACM (2007)Giesl, J., Arts, T.: Verification of Erlang Processes by Dependency Pairs. Appl. Algebra Eng. Commun. Comput. 12(1/2), 39–72 (2001)Hanus, M. (ed.): Curry: An integrated functional logic language (vers. 0.8.3) (2012), http://www.curry-language.orgHuch, F.: Verification of Erlang Programs using Abstract Interpretation and Model Checking. In: Rémi, D., Lee, P. (eds.) Proc. of ICFP 1999, pp. 261–272. ACM (1999)J.-M., H.: Canonical forms and unification. In: Bibel, W., Kowalski, R. (eds.) 5th Conference on Automated Deduction Les Arcs. LNCS, pp. 318–334. Springer, Heidelberg (1980)Leucker, M., Noll, T.: Rewriting Logic as a Framework for Generic Verification Tools. Electr. Notes Theor. Comput. Sci. 36, 121–137 (2000)Meseguer, J.: Conditioned Rewriting Logic as a United Model of Concurrency. Theor. Comput. Sci. 96(1), 73–155 (1992)Neuhäußer, M.R., Noll, T.: Abstraction and Model Checking of Core Erlang Programs in Maude. Electr. Notes Theor. Comput. Sci. 176(4), 147–163 (2007)Nishida, N., Vidal, G.: A finite representation of the narrowing space. In: Proc. of the 23th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR 2013). Technical Report TR-11-13, Universidad Complutense de Madrid, pp. 113–128 (To appear in Springer LNCS, 2013). http://users.dsic.upv.es/~gvidal/Noll, T.: A Rewriting Logic Implementation of Erlang. Electr. Notes Theor. Comput. Sci. 44(2), 206–224 (2001)Noll, T.: Equational Abstractions for Model Checking Erlang Programs. Electr. Notes Theor. Comput. Sci. 118, 145–162 (2005)Noll, T.G., Fredlund, L., Gurov, D.: The Erlang Verification Tool. In: Margaria, T., Yi, W. (eds.) TACAS 2001. LNCS, vol. 2031, pp. 582–586. Springer, Heidelberg (2001)Roy, C.K.: Thomas Noll, Banani Roy, and James R. Cordy. Towards automatic verification of Erlang programs by pi-calculus translation. In: Feeley,M., Trinder, P.W. (eds.) Proc. of the 2006 ACM SIGPLAN Workshop on Erlang, pp. 38–50. ACM (2006)Slagle, J.R.: Automated theorem-proving for theories with simplifiers, commutativity and associativity. Journal of the ACM 21(4), 622–642 (1974)Svensson, H., Fredlund, L.-A.: A more accurate semantics for distributed Erlang. In: Thompson, S.J., Fredlund. L.-A., (eds.) Proceedings of the 2007 ACM SIGPLAN Workshop on Erlang, pp. 43–54. ACM (2007)Vidal, G.: Closed symbolic execution for verifying program termination. In: Proc. of the 12th IEEE International Working Conference on Source Code Analysis and Manipulation (SCAM 2012), pp. 34–43. IEEE (2012)Visser, W., Havelund, K., Brat, G.P., Park, S., Lerda, F.: Model checking programs. Autom. Softw. Eng. 10(2), 203–232 (2003

Assisted evolution enables HIV-1 to overcome a high trim5α-imposed genetic barrier to rhesus macaque tropism

Diversification of antiretroviral factors during host evolution has erected formidable barriers to cross-species retrovirus transmission. This phenomenon likely protects humans from infection by many modern retroviruses, but it has also impaired the development of primate models of HIV-1 infection. Indeed, rhesus macaques are resistant to HIV-1, in part due to restriction imposed by the TRIM5α protein (rhTRIM5α). Initially, we attempted to derive rhTRIM5α-resistant HIV-1 strains using two strategies. First, HIV-1 was passaged in engineered human cells expressing rhTRIM5α. Second, a library of randomly mutagenized capsid protein (CA) sequences was screened for mutations that reduced rhTRIM5α sensitivity. Both approaches identified several individual mutations in CA that reduced rhTRIM5α sensitivity. However, neither approach yielded mutants that were fully resistant, perhaps because the locations of the mutations suggested that TRIM5α recognizes multiple determinants on the capsid surface. Moreover, even though additive effects of various CA mutations on HIV-1 resistance to rhTRIM5α were observed, combinations that gave full resistance were highly detrimental to fitness. Therefore, we employed an 'assisted evolution' approach in which individual CA mutations that reduced rhTRIM5α sensitivity without fitness penalties were randomly assorted in a library of viral clones containing synthetic CA sequences. Subsequent passage of the viral library in rhTRIM5α-expressing cells resulted in the selection of individual viral species that were fully fit and resistant to rhTRIM5α. These viruses encoded combinations of five mutations in CA that conferred complete or near complete resistance to the disruptive effects of rhTRIM5α on incoming viral cores, by abolishing recognition of the viral capsid. Importantly, HIV-1 variants encoding these CA substitutions and SIVmac239 Vif replicated efficiently in primary rhesus macaque lymphocytes. These findings demonstrate that rhTRIM5α is difficult to but not impossible to evade, and doing so should facilitate the development of primate models of HIV-1 infection

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

Morphology, ultrastructure and molecular characterisation of Spiroxys japonica Morishita, 1926 (Spirurida: Gnathostomatidae) from Pelophylax nigromaculatus (Hallowell) (Amphibia: Ranidae)

Gnathostomatid nematodes identified morphologically as Spiroxys japonica Morishita, 1926 were collected from the dark-spotted frog Pelophylax nigromaculatus (Hallowell) (Amphibia: Ranidae) in China. Light and scanning electron microscopy were used to study the morphology of this species in detail. Previously unreported morphological features are revealed and others corrected. In addition, adult nematodes of S. japonica collected from P. nigromaculatus and Spiroxys hanzaki Hasegawa, Miyata & Doi, 1998 collected from Andrias japonicus (Temminck) (Caudata: Cryptobranchidae) in China and Japan, respectively, and the third-stage larva of S. japonica collected from Lithobates catesbeianus (Shaw) (Anura: Ranidae) in Japan, were characterised using molecular methods by sequencing and analysing ribosomal [large ribosomal DNA (18S) and internal transcribed space] and mitochondrial [cytochrome c oxidase subunit 1] target regions, respectively. The new morphological and genetic data contributes to a more accurate diagnosis of this hitherto little known nematode genus

Experimental mutation-accumulation on the X chromosome of Drosophila melanogaster reveals stronger selection on males than females

<p>Abstract</p> <p>Background</p> <p>Sex differences in the magnitude or direction of mutational effect may be important to a variety of population processes, shaping the mutation load and affecting the cost of sex itself. These differences are expected to be greatest after sexual maturity. Mutation-accumulation (MA) experiments provide the most direct way to examine the consequences of new mutations, but most studies have focused on juvenile viability without regard to sex, and on autosomes rather than sex chromosomes; both adult fitness and X-linkage have been little studied. We therefore investigated the effects of 50 generations of X-chromosome mutation accumulation on the fitness of males and females derived from an outbred population of <it>Drosophila melanogaster</it>.</p> <p>Results</p> <p>Fitness declined rapidly in both sexes as a result of MA, but adult males showed markedly greater fitness loss relative to their controls compared to females expressing identical genotypes, even when females were made homozygous for the X. We estimate that these mutations are partially additive (h ~ 0.3) in females. In addition, the majority of new mutations appear to harm both males and females.</p> <p>Conclusions</p> <p>Our data helps fill a gap in our understanding of the consequences of sexual selection for genetic load, and suggests that stronger selection on males may indeed purge deleterious mutations affecting female fitness.</p