YAPA: A generic tool for computing intruder knowledge

Reasoning about the knowledge of an attacker is a necessary step in many formal analyses of security protocols. In the framework of the applied pi calculus, as in similar languages based on equational logics, knowledge is typically expressed by two relations: deducibility and static equivalence. Several decision procedures have been proposed for these relations under a variety of equational theories. However, each theory has its particular algorithm, and none has been implemented so far. We provide a generic procedure for deducibility and static equivalence that takes as input any convergent rewrite system. We show that our algorithm covers most of the existing decision procedures for convergent theories. We also provide an efficient implementation, and compare it briefly with the tools ProVerif and KiSs

Vocal development in a large‐scale crosslinguistic corpus

This study evaluates whether early vocalizations develop in similar ways in children across diverse cultural contexts. We analyze data from daylong audio recordings of 49 children (1–36 months) from five different language/cultural backgrounds. Citizen scientists annotated these recordings to determine if child vocalizations contained canonical transitions or not (e.g., “ba” vs. “ee”). Results revealed that the proportion of clips reported to contain canonical transitions increased with age. Furthermore, this proportion exceeded 0.15 by around 7 months, replicating and extending previous findings on canonical vocalization development but using data from the natural environments of a culturally and linguistically diverse sample. This work explores how crowdsourcing can be used to annotate corpora, helping establish developmental milestones relevant to multiple languages and cultures. Lower inter‐annotator reliability on the crowdsourcing platform, relative to more traditional in‐lab expert annotators, means that a larger number of unique annotators and/or annotations are required, and that crowdsourcing may not be a suitable method for more fine‐grained annotation decisions. Audio clips used for this project are compiled into a large‐scale infant vocalization corpus that is available for other researchers to use in future work

Experiência de utilização de XML no SMS.

XML e sua utilização em aplicações de bioinformática. Utilização de XML no módulo JPD do SMS. Discussão e trabalhos futuros.bitstream/CNPTIA/9891/1/comuntec32.pdfAcesso em: 30 maio 2008

Scattering of second sound waves by quantum vorticity

A new method of detection and measurement of quantum vorticity by scattering second sound off quantized vortices in superfluid Helium is suggested. Theoretical calculations of the relative amplitude of the scattered second sound waves from a single quantum vortex, a vortex ring, and bulk vorticity are presented. The relevant estimates show that an experimental verification of the method is feasible. Moreover, it can even be used for the detection of a single quantum vortex.Comment: Latex file, 9 page

Thromboembolism and bleeding in systemic amyloidosis: a review

The assessment of both thromboembolic and haemorrhagic risks and their management in systemic amyloidosis have been poorly emphasized so far. This narrative review summarizes main evidence from literature with clinical perspective. The rate of thromboembolic events is as high as 5–10% amyloidosis patients, at least in patients with cardiac involvement, with deleterious impact on prognosis. The most known pro-thrombotic factors are heart failure, atrial fibrillation, and atrial myopathy. Atrial fibrillation could occur in 20% to 75% of systemic amyloidosis patients. Cardiac thrombi are frequently observed in patients, particularly in immunoglobulin light chains (AL) amyloidosis, up to 30%, and it is advised to look for them systematically before cardioversion. In AL amyloidosis, nephrotic syndrome and the use of immunomodulatory drugs also favour thrombosis. On the other hand, the bleeding risk increases because of frequent amyloid digestive involvement as well as factor X deficiency, renal failure, and increased risk of dysautonomia-related fall

SMSLib - biblioteca C++ do Sting Millennium Suite.

Organização lógica do SMS. Descrição da SMSLib. Leitura de arquivos PDB. Leitura de arquivos HSSP. Leitura de arquivos com parâmetros simples. Cálculo e leitura de contatos. Cálculo e leitura de Dihedral Angels.bitstream/CNPTIA/9898/1/comuntec39.pdfAcesso em: 30 maio 2008

A Cryogenic High-Reynolds Turbulence Experiment at CERN

The potential of cryogenic helium flows for studying high-Reynolds number turbulence in the laboratory has been recognised for a long time and implemented in several small-scale hydrodynamic experiments. With its large superconducting particle accelerators and detector magnets, CERN, the European Laboratory for Particle Physics, has become a major world center in helium cryogenics, with several large helium refrigerators having capacities up to 18 kW @ 4.5 K. Combining a small fraction of these resources with the expertise of three laboratories at the forefront of turbulence research, has led to the design, swift implementation, and successful operation of GReC (Grands Reynolds Cryogéniques) a large axisymmetric turbulent-jet experiment. With flow-rates up to 260 g/s of gaseous helium at ~ 5 K and atmospheric pressure, Reynolds numbers up to 107 have been achieved in a 4.6 m high, 1.4 m diameter cryostat. This paper presents the results of the first runs and describes the experimental set-up comprehensively equipped with "hot" wire micro-anemometers, acoustic scattering vorticity measurements and a large-bandwidth data acquisition system

STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

Sting Millennium suite intrinsics. SMS organization. Sting Millennium Modes. Sting Millennium Modules. Millennium Features. Example of Sting Millennium Application.Na publicação: Paula R. Kuser

Protocol analysis modulo combination of theories: A case study in Maude-NPA

There is a growing interest in formal methods and tools to analyze cryptographic protocols modulo algebraic properties of their underlying cryptographic functions. It is well-known that an intruder who uses algebraic equivalences of such functions can mount attacks that would be impossible if the cryptographic functions did not satisfy such equivalences. In practice, however, protocols use a collection of well-known functions, whose algebraic properties can naturally be grouped together as a union of theories E 1... ¿ n. Reasoning symbolically modulo the algebraic properties E 1... ¿ n requires performing (E 1... ¿ n)-unification. However, even if a unification algorithm for each individual E i is available, this requires combining the existing algorithms by methods that are highly non-deterministic and have high computational cost. In this work we present an alternative method to obtain unification algorithms for combined theories based on variant narrowing. Although variant narrowing is less efficient at the level of a single theory E i, it does not use any costly combination method. Furthermore, it does not require that each E i has a dedicated unification algorithm in a tool implementation. We illustrate the use of this method in the Maude-NPA tool by means of a well-known protocol requiring the combination of three distinct equational theories. © 2011 Springer-Verlag.R. Sasse and J. Meseguer have been partially supported by NSF Grants CNS0716638, CNS-0831064 and CNS-0904749. S. Escobar has been partially supported by the EU (FEDER) and the Spanish MEC/MICINN under grant TIN 2007-68093- C02-02. C. Meadows has been partially supported by NSF Grant CNS-0904749National Science Foundation, EEUUSasse, R.; Escobar Román, S.; Meadows, C.; Meseguer, J. (2011). Protocol analysis modulo combination of theories: A case study in Maude-NPA. En Security and Trust Management. Springer Verlag (Germany). 6710:163-178. doi:10.1007/978-3-642-22444-7_11S1631786710Abadi, M., Cortier, V.: Deciding knowledge in security protocols under equational theories. Theoretical Computer Science 367(1-2), 2–32 (2006)Armando, A., Basin, D.A., Boichut, Y., Chevalier, Y., Compagna, L., Cuéllar, J., Drielsma, P.H., Héam, P.-C., Kouchnarenko, O., Mantovani, J., Mödersheim, S., von Oheimb, D., Rusinowitch, M., Santiago, J., Turuani, M., Viganò, L., Vigneron, L.: The avispa tool for the automated validation of internet security protocols and applications. In: Etessami, K., Rajamani, S.K. (eds.) CAV 2005. LNCS, vol. 3576, pp. 281–285. Springer, Heidelberg (2005)Baader, F., Schulz, K.U.: Unification in the union of disjoint equational theories: Combining decision procedures. In: Kapur, D. (ed.) CADE 1992. LNCS, vol. 607, pp. 50–65. Springer, Heidelberg (1992)Basin, D.A., Mödersheim, S., Viganò, L.: An on-the-fly model-checker for security protocol analysis. In: Snekkenes, E., Gollmann, D. (eds.) ESORICS 2003. LNCS, vol. 2808, pp. 253–270. Springer, Heidelberg (2003)Baudet, M., Cortier, V., Delaune, S.: YAPA: A generic tool for computing intruder knowledge. In: Treinen, R. (ed.) RTA 2009. LNCS, vol. 5595, pp. 148–163. Springer, Heidelberg (2009)Blanchet, B.: An efficient cryptographic protocol verifier based on prolog rules. In: CSFW, pp. 82–96. IEEE Computer Society, Los Alamitos (2001)Bursuc, S., Comon-Lundh, H.: Protocol security and algebraic properties: Decision results for a bounded number of sessions. In: Treinen, R. (ed.) RTA 2009. LNCS, vol. 5595, pp. 133–147. Springer, Heidelberg (2009)Chevalier, Y., Küsters, R., Rusinowitch, M., Turuani, M.: An NP decision procedure for protocol insecurity with XOR. In: LICS, pp. 261–270. IEEE Computer Society, Los Alamitos (2003)Chevalier, Y., Rusinowitch, M.: Hierarchical combination of intruder theories. Inf. Comput. 206(2-4), 352–377 (2008)Chevalier, Y., Rusinowitch, M.: Symbolic protocol analysis in the union of disjoint intruder theories: Combining decision procedures. Theor. Comput. Sci. 411(10), 1261–1282 (2010)Ciobâcă, Ş., Delaune, S., Kremer, S.: Computing knowledge in security protocols under convergent equational theories. In: Schmidt, R.A. (ed.) CADE-22. LNCS, vol. 5663, pp. 355–370. Springer, Heidelberg (2009)Comon-Lundh, H., Delaune, S.: The finite variant property: How to get rid of some algebraic properties. In: Giesl, J. (ed.) RTA 2005. LNCS, vol. 3467, pp. 294–307. Springer, Heidelberg (2005)Cortier, V., Delaitre, J., Delaune, S.: Safely composing security protocols. In: Arvind, V., Prasad, S. (eds.) FSTTCS 2007. LNCS, vol. 4855, pp. 352–363. Springer, Heidelberg (2007)Cremers, C.J.F.: The scyther tool: Verification, falsification, and analysis of security protocols. In: Gupta, A., Malik, S. (eds.) CAV 2008. LNCS, vol. 5123, pp. 414–418. Springer, Heidelberg (2008)Escobar, S., Meadows, C., Meseguer, J.: A rewriting-based inference system for the NRL protocol analyzer and its meta-logical properties. Theoretical Computer Science 367(1-2), 162–202 (2006)Escobar, S., Meadows, C., Meseguer, J.: Maude-NPA: Cryptographic protocol analysis modulo equational properties. In: Aldini, A., Barthe, G., Gorrieri, R. (eds.) FOSAD 2007/2008/2009 Tutorial Lectures. LNCS, vol. 5705, pp. 1–50. Springer, Heidelberg (2009)Escobar, S., Meseguer, J., Sasse, R.: Effectively checking or disproving the finite variant property. Technical Report UIUCDCS-R-2008-2960, Department of Computer Science - University of Illinois at Urbana-Champaign (April 2008)Escobar, S., Meseguer, J., Sasse, R.: Effectively checking the finite variant property. In: Voronkov, A. (ed.) RTA 2008. LNCS, vol. 5117, pp. 79–93. Springer, Heidelberg (2008)Escobar, S., Meseguer, J., Sasse, R.: Variant narrowing and equational unification. Electr. Notes Theor. Comput. Sci. 238(3), 103–119 (2009)Escobar, S., Sasse, R., Meseguer, J.: Folding variant narrowing and optimal variant termination. In: Ölveczky, P.C. (ed.) WRLA 2010. LNCS, vol. 6381, pp. 52–68. Springer, Heidelberg (2010)Fabrega, F.J.T., Herzog, J., Guttman, J.: Strand Spaces: What Makes a Security Protocol Correct? Journal of Computer Security 7, 191–230 (1999)Guo, Q., Narendran, P.: Unification and matching modulo nilpotence. In: CADE-13. LNCS, vol. 1104, pp. 261–274. Springer, Heidelberg (1996)Harkins, D., Carrel, D.: The Internet Key Exchange (IKE), IETF RFC 2409, (November 1998)Jouannaud, J.-P., Kirchner, C., Kirchner, H.: Incremental construction of unification algorithms in equational theories. In: Díaz, J. (ed.) ICALP 1983. LNCS, vol. 154, pp. 361–373. Springer, Heidelberg (1983)Küsters, R., Truderung, T.: Reducing protocol analysis with xor to the xor-free case in the Horn theory based approach. 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Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

[Image: see text] Proteogenomics has the potential to advance genome annotation through high quality peptide identifications derived from mass spectrometry experiments, which demonstrate a given gene or isoform is expressed and translated at the protein level. This can advance our understanding of genome function, discovering novel genes and gene structure that have not yet been identified or validated. Because of the high-throughput shotgun nature of most proteomics experiments, it is essential to carefully control for false positives and prevent any potential misannotation. A number of statistical procedures to deal with this are in wide use in proteomics, calculating false discovery rate (FDR) and posterior error probability (PEP) values for groups and individual peptide spectrum matches (PSMs). These methods control for multiple testing and exploit decoy databases to estimate statistical significance. Here, we show that database choice has a major effect on these confidence estimates leading to significant differences in the number of PSMs reported. We note that standard target:decoy approaches using six-frame translations of nucleotide sequences, such as assembled transcriptome data, apparently underestimate the confidence assigned to the PSMs. The source of this error stems from the inflated and unusual nature of the six-frame database, where for every target sequence there exists five “incorrect” targets that are unlikely to code for protein. The attendant FDR and PEP estimates lead to fewer accepted PSMs at fixed thresholds, and we show that this effect is a product of the database and statistical modeling and not the search engine. A variety of approaches to limit database size and remove noncoding target sequences are examined and discussed in terms of the altered statistical estimates generated and PSMs reported. These results are of importance to groups carrying out proteogenomics, aiming to maximize the validation and discovery of gene structure in sequenced genomes, while still controlling for false positives