Stable fourfold configurations for small vacancy clusters in silicon from ab initio calculations

Using density-functional-theory calculations, we have identified new stable configurations for tri-, tetra-, and penta-vacancies in silicon. These new configurations consist of combinations of a ring-hexavacancy with three, two, or one interstitial atoms, respectively, such that all atoms remain fourfold. As a result, their formation energies are lower by 0.6, 1.0, and 0.6 eV, respectively, than the ``part of a hexagonal ring'' configurations, believed up to now to be the lowest-energy states

Proving Nontermination via safety

We show how the problem of nontermination proving can be reduced to a question of underapproximation search guided by a safety prover. This reduction leads to new nontermination proving implementation strategies based on existing tools for safety proving. Our preliminary implementation beats existing tools. Furthermore, our approach leads to easy support for programs with unbounded nondeterminism

Phototesting and photoprotection in LE

Photosensitivity and induction of skin lesions following UV radiation is a common problem of patients with cutaneous and systemic forms of lupus erythematosus. The detrimental effect of UV radiation to patients with lupus erythematosus was already recognized in the last century. Skin lesions can now be provoked under standardized conditions allowing the diagnosis and classification of patients with photosensitive disorders. The aim of this review is to give an overview on the history, test procedure and test results in patients with lupus erythematosus

Models for logics and conditional constraints in automated proofs of termination

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-13770-4_3Reasoning about termination of declarative programs, which are described by means of a computational logic, requires the definition of appropriate abstractions as semantic models of the logic, and also handling the conditional constraints which are often obtained. The formal treatment of such constraints in automated proofs, often using numeric interpretations and (arithmetic) constraint solving can greatly benefit from appropriate techniques to deal with the conditional (in)equations at stake. Existing results from linear algebra or real algebraic geometry are useful to deal with them but have received only scant attention to date. We investigate the definition and use of numeric models for logics and the resolution of linear and algebraic conditional constraints as unifying techniques for proving termination of declarative programs.Developed during a sabbatical year at UIUC. Supported by projects NSF CNS13-19109, MINECO TIN2010-21062-C02-02 and TIN2013-45732-C4-1-P, and GV BEST/2014/026 and PROMETEO/2011/052.Lucas Alba, S.; Meseguer, J. (2014). Models for logics and conditional constraints in automated proofs of termination. En Artificial Intelligence and Symbolic Computation. Springer Verlag (Germany). 9-20. https://doi.org/10.1007/978-3-319-13770-4_3S920Alarcón, B., Gutiérrez, R., Lucas, S., Navarro-Marset, R.: Proving Termination Properties with mu-term. In: Johnson, M., Pavlovic, D. (eds.) AMAST 2010. LNCS, vol. 6486, pp. 201–208. Springer, Heidelberg (2011)Alarcón, B., Lucas, S., Navarro-Marset, R.: Using Matrix Interpretations over the Reals in Proofs of Termination. In: Proc. of PROLE 2009, pp. 255–264 (2009)Clavel, M., Durán, F., Eker, S., Lincoln, P., Martí-Oliet, N., Meseguer, J., Talcott, C. (eds.): All About Maude - A High-Performance Logical Framework. LNCS, vol. 4350. Springer, Heidelberg (2007)Contejean, E., Marché, C., Tomás, A.-P., Urbain, X.: Mechanically proving termination using polynomial interpretations. J. of Aut. Reas. 34(4), 325–363 (2006)Endrullis, J., Waldmann, J., Zantema, H.: Matrix Interpretations for Proving Termination of Term Rewriting. J. of Aut. Reas. 40(2-3), 195–220 (2008)Fuhs, C., Giesl, J., Middeldorp, A., Schneider-Kamp, P., Thiemann, R., Zankl, H.: Maximal Termination. In: Voronkov, A. (ed.) RTA 2008. LNCS, vol. 5117, pp. 110–125. Springer, Heidelberg (2008)Futatsugi, K., Diaconescu, R.: CafeOBJ Report. AMAST Series. World Scientific (1998)Hudak, P., Peyton-Jones, S.J., Wadler, P.: Report on the Functional Programming Language Haskell: a non–strict, purely functional language. Sigplan Notices 27(5), 1–164 (1992)Lucas, S.: Context-sensitive computations in functional and functional logic programs. Journal of Functional and Logic Programming 1998(1), 1–61 (1998)Lucas, S.: Polynomials over the reals in proofs of termination: from theory to practice. RAIRO Theoretical Informatics and Applications 39(3), 547–586 (2005)Lucas, S., Marché, C., Meseguer, J.: Operational termination of conditional term rewriting systems. Information Processing Letters 95, 446–453 (2005)Lucas, S., Meseguer, J.: Proving Operational Termination of Declarative Programs in General Logics. In: Proc. of PPDP 2014, pp. 111–122. ACM Digital Library (2014)Lucas, S., Meseguer, J.: 2D Dependency Pairs for Proving Operational Termination of CTRSs. In: Proc. of WRLA 2014. LNCS, vol. 8663 (to appear, 2014)Lucas, S., Meseguer, J., Gutiérrez, R.: Extending the 2D DP Framework for CTRSs. In: Selected papers of LOPSTR 2014. LNCS (to appear, 2015)Meseguer, J.: General Logics. In: Ebbinghaus, H.-D., et al. (eds.) Logic Colloquium 1987, pp. 275–329. North-Holland (1989)Nguyen, M.T., de Schreye, D., Giesl, J., Schneider-Kamp, P.: Polytool: Polynomial interpretations as a basis for termination of logic programs. Theory and Practice of Logic Programming 11(1), 33–63 (2011)Ohlebusch, E.: Advanced Topics in Term Rewriting. Springer (April 2002)Prestel, A., Delzell, C.N.: Positive Polynomials. In: From Hilbert’s 17th Problem to Real Algebra. Springer, Berlin (2001)Podelski, A., Rybalchenko, A.: A Complete Method for the Synthesis of Linear Ranking Functions. In: Steffen, B., Levi, G. (eds.) VMCAI 2004. LNCS, vol. 2937, pp. 239–251. Springer, Heidelberg (2004)Schrijver, A.: Theory of linear and integer programming. John Wiley & Sons (1986)Zantema, H.: Termination of Context-Sensitive Rewriting. In: Comon, H. (ed.) RTA 1997. LNCS, vol. 1232, pp. 172–186. Springer, Heidelberg (1997

Analyzing program termination and complexity automatically with AProVE

In this system description, we present the tool AProVE for automatic termination and complexity proofs of Java, C, Haskell, Prolog, and rewrite systems. In addition to classical term rewrite systems (TRSs), AProVE also supports rewrite systems containing built-in integers (int-TRSs). To analyze programs in high-level languages, AProVE automatically converts them to (int-)TRSs. Then, a wide range of techniques is employed to prove termination and to infer complexity bounds for the resulting rewrite systems. The generated proofs can be exported to check their correctness using automatic certifiers. To use AProVE in software construction, we present a corresponding plug-in for the popular Eclipse software development environment

ESR observations of paramagnetic centers in intrinsic hydrogenated microcrystalline silicon

Paramagnetic centers in hydrogenated microcrystalline silicon, µc-Si:H have been studied using dark and light-induced electron-spin resonance (ESR). In dark ESR measurements only one center is observed. The g values obtained empirically from powder-pattern line-shape simulations are g=2.0096 and g'=2.0031. We suggest that this center may be due to defects in the crystalline phase. During illumination at low temperatures, an additional ESR signal appears. This signal is best described by two powder patterns indicating the presence of two centers. One center is asymmetric (gi=1.999, g'=1.996), while the other is characterized by large, unresolved broadening such that unique g values cannot be obtained. The average g value for this center is 1.998. The light-induced signal, which we interpret as coming from carriers trapped in the band tails at the crystalline grain boundaries, remains for at least several minutes after the light is turned off. Although the time scales of the decay curves are very different for two samples prepared by different techniques, both decays can be fitted using the assumption of recombination due to distant pairs of electrons and holes trapped in localized band-tail states

An analysis of waves underlying grid cell firing in the medial enthorinal cortex

Layer II stellate cells in the medial enthorinal cortex (MEC) express hyperpolarisation-activated cyclic-nucleotide-gated (HCN) channels that allow for rebound spiking via an I_h current in response to hyperpolarising synaptic input. A computational modelling study by Hasselmo [2013 Neuronal rebound spiking, resonance frequency and theta cycle skipping may contribute to grid cell firing in medial entorhinal cortex. Phil. Trans. R. Soc. B 369: 20120523] showed that an inhibitory network of such cells can support periodic travelling waves with a period that is controlled by the dynamics of the I_h current. Hasselmo has suggested that these waves can underlie the generation of grid cells, and that the known difference in I_h resonance frequency along the dorsal to ventral axis can explain the observed size and spacing between grid cell firing fields. Here we develop a biophysical spiking model within a framework that allows for analytical tractability. We combine the simplicity of integrate-and-fire neurons with a piecewise linear caricature of the gating dynamics for HCN channels to develop a spiking neural field model of MEC. Using techniques primarily drawn from the field of nonsmooth dynamical systems we show how to construct periodic travelling waves, and in particular the dispersion curve that determines how wave speed varies as a function of period. This exhibits a wide range of long wavelength solutions, reinforcing the idea that rebound spiking is a candidate mechanism for generating grid cell firing patterns. Importantly we develop a wave stability analysis to show how the maximum allowed period is controlled by the dynamical properties of the I_h current. Our theoretical work is validated by numerical simulations of the spiking model in both one and two dimensions

The Influence of Markov Decision Process Structure on the Possible Strategic Use of Working Memory and Episodic Memory

Researchers use a variety of behavioral tasks to analyze the effect of biological manipulations on memory function. This research will benefit from a systematic mathematical method for analyzing memory demands in behavioral tasks. In the framework of reinforcement learning theory, these tasks can be mathematically described as partially-observable Markov decision processes. While a wealth of evidence collected over the past 15 years relates the basal ganglia to the reinforcement learning framework, only recently has much attention been paid to including psychological concepts such as working memory or episodic memory in these models. This paper presents an analysis that provides a quantitative description of memory states sufficient for correct choices at specific decision points. Using information from the mathematical structure of the task descriptions, we derive measures that indicate whether working memory (for one or more cues) or episodic memory can provide strategically useful information to an agent. In particular, the analysis determines which observed states must be maintained in or retrieved from memory to perform these specific tasks. We demonstrate the analysis on three simplified tasks as well as eight more complex memory tasks drawn from the animal and human literature (two alternation tasks, two sequence disambiguation tasks, two non-matching tasks, the 2-back task, and the 1-2-AX task). The results of these analyses agree with results from quantitative simulations of the task reported in previous publications and provide simple indications of the memory demands of the tasks which can require far less computation than a full simulation of the task. This may provide a basis for a quantitative behavioral stoichiometry of memory tasks

Revisiting the pH-gated conformational switch on the activities of HisKA-family histidine kinases

Histidine is a versatile residue playing key roles in enzyme catalysis thanks to the chemistry of its imidazole group that can serve as nucleophile, general acid or base depending on its protonation state. In bacteria, signal transduction relies on two-component systems (TCS) which comprise a sensor histidine kinase (HK) containing a phosphorylatable catalytic His with phosphotransfer and phosphatase activities over an effector response regulator. Recently, a pH-gated model has been postulated to regulate the phosphatase activity of HisKA HKs based on the pH-dependent rotamer switch of the phosphorylatable His. Here, we have revisited this model from a structural and functional perspective on HK853-RR468 and EnvZ-OmpR TCS, the prototypical HisKA HKs. We have found that the rotamer of His is not influenced by the environmental pH, ruling out a pH-gated model and confirming that the chemistry of the His is responsible for the decrease in the phosphatase activity at acidic pH

The protein histidine phosphatase LHPP is a tumour suppressor

Histidine phosphorylation, the so-called hidden phosphoproteome, is a poorly characterized post-translational modification of proteins. Here we describe a role of histidine phosphorylation in tumorigenesis. Proteomic analysis of 12 tumours from an mTOR-driven hepatocellular carcinoma mouse model revealed that NME1 and NME2, the only known mammalian histidine kinases, were upregulated. Conversely, expression of the putative histidine phosphatase LHPP was downregulated specifically in the tumours. We demonstrate that LHPP is indeed a protein histidine phosphatase. Consistent with these observations, global histidine phosphorylation was significantly upregulated in the liver tumours. Sustained, hepatic expression of LHPP in the hepatocellular carcinoma mouse model reduced tumour burden and prevented the loss of liver function. Finally, in patients with hepatocellular carcinoma, low expression of LHPP correlated with increased tumour severity and reduced overall survival. Thus, LHPP is a protein histidine phosphatase and tumour suppressor, suggesting that deregulated histidine phosphorylation is oncogenic