Hierarchic Superposition Revisited

Many applications of automated deduction require reasoning in first-order logic modulo background theories, in particular some form of integer arithmetic. A major unsolved research challenge is to design theorem provers that are "reasonably complete" even in the presence of free function symbols ranging into a background theory sort. The hierarchic superposition calculus of Bachmair, Ganzinger, and Waldmann already supports such symbols, but, as we demonstrate, not optimally. This paper aims to rectify the situation by introducing a novel form of clause abstraction, a core component in the hierarchic superposition calculus for transforming clauses into a form needed for internal operation. We argue for the benefits of the resulting calculus and provide two new completeness results: one for the fragment where all background-sorted terms are ground and another one for a special case of linear (integer or rational) arithmetic as a background theory

Sampling-based path planning for multi-robot systems with co-safe linear temporal logic specifications

© 2017, Springer International Publishing AG. This paper addresses the problem of path planning for multiple robots under high-level specifications given as syntactically co-safe linear temporal logic formulae. Most of the existing solutions use the notion of abstraction to obtain a discrete transition system that simulates the dynamics of the robot. Nevertheless, these solutions have poor scalability with the dimension of the configuration space of the robots. For problems with a single robot, sampling-based methods have been presented as a solution to alleviate this limitation. The proposed solution extends the idea of sampling methods to the multiple robot case. The method samples the configuration space of the robots to incrementally constructs a transition system that models the motion of all the robots as a group. This transition system is then combined with a Büchi automaton, representing the specification, in a Cartesian product. The product is updated with each expansion of the transition system until a solution is found. We also present a new algorithm that improves the performance of the proposed method by guiding the expansion of the transition system. The method is demonstrated with examples considering different number of robots and specifications

A Theory of Cheap Control in Embodied Systems

We present a framework for designing cheap control architectures for embodied agents. Our derivation is guided by the classical problem of universal approximation, whereby we explore the possibility of exploiting the agent's embodiment for a new and more efficient universal approximation of behaviors generated by sensorimotor control. This embodied universal approximation is compared with the classical non-embodied universal approximation. To exemplify our approach, we present a detailed quantitative case study for policy models defined in terms of conditional restricted Boltzmann machines. In contrast to non-embodied universal approximation, which requires an exponential number of parameters, in the embodied setting we are able to generate all possible behaviors with a drastically smaller model, thus obtaining cheap universal approximation. We test and corroborate the theory experimentally with a six-legged walking machine. The experiments show that the sufficient controller complexity predicted by our theory is tight, which means that the theory has direct practical implications. Keywords: cheap design, embodiment, sensorimotor loop, universal approximation, conditional restricted Boltzmann machineComment: 27 pages, 10 figure

A comparison of transgenic rodent mutation and in vivo comet assay responses for 91 chemicals.

A database of 91 chemicals with published data from both transgenic rodent mutation (TGR) and rodent comet assays has been compiled. The objective was to compare the sensitivity of the two assays for detecting genotoxicity. Critical aspects of study design and results were tabulated for each dataset. There were fewer datasets from rats than mice, particularly for the TGR assay, and therefore, results from both species were combined for further analysis. TGR and comet responses were compared in liver and bone marrow (the most commonly studied tissues), and in stomach and colon evaluated either separately or in combination with other GI tract segments. Overall positive, negative, or equivocal test results were assessed for each chemical across the tissues examined in the TGR and comet assays using two approaches: 1) overall calls based on weight of evidence (WoE) and expert judgement, and 2) curation of the data based on a priori acceptability criteria prior to deriving final tissue specific calls. Since the database contains a high prevalence of positive results, overall agreement between the assays was determined using statistics adjusted for prevalence (using AC1 and PABAK). These coefficients showed fair or moderate to good agreement for liver and the GI tract (predominantly stomach and colon data) using WoE, reduced agreement for stomach and colon evaluated separately using data curation, and poor or no agreement for bone marrow using both the WoE and data curation approaches. Confidence in these results is higher for liver than for the other tissues, for which there were less data. Our analysis finds that comet and TGR generally identify the same compounds (mainly potent mutagens) as genotoxic in liver, stomach and colon, but not in bone marrow. However, the current database content precluded drawing assay concordance conclusions for weak mutagens and non-DNA reactive chemicals

HD molecules at high redshift: The absorption system at z=2.3377 towards Q 1232+082

We present a detailed analysis of the H_2 and HD absorption lines detected in the Damped Lyman-alpha (DLA) system at z_abs=2.3377 towards the quasar Q1232+082. We show that this intervening cloud has a covering factor smaller than unity and covers only part of the QSO broad emission line region. The zero flux level has to be corrected at the position of the saturated H_2 and optically thin HD lines by about 10%. We accurately determine the Doppler parameter for HD and CI lines (b = 1.86+/-0.20 km/s). We find a ratio N(HD)/N(H_2)=(7.1 +3.7 -2.2)x10^-5 that is significantly higher than what is observed in molecular clouds of the Galaxy. Chemical models suggest that in the physical conditions prevailing in the central part of molecular clouds, deuterium and hydrogen are mostly in their molecular forms. Assuming this is true, we derive D/H = (3.6 +1.9 -1.1)x10^-5. This implies that the corresponding baryon density of the Universe is \Omega_b h^2 = (0.0182 +0.0047 -0.0042). This value coincides within 1\sigma with that derived from observations of the CMBR as well as from observations of the D/H atomic ratio in low-metallicity QSO absorption line systems. The observation of HD at high redshift is therefore a promising independent method to constrain \Omega_b. This observation indicates as well a low astration factor of deuterium. This can be interpreted as the consequence of an intense infall of primordial gas onto the associated galaxy.Comment: 8 pages, 7 figures, 3 tables. Accepted for publication in MNRA

Invariant Synthesis for Incomplete Verification Engines

We propose a framework for synthesizing inductive invariants for incomplete verification engines, which soundly reduce logical problems in undecidable theories to decidable theories. Our framework is based on the counter-example guided inductive synthesis principle (CEGIS) and allows verification engines to communicate non-provability information to guide invariant synthesis. We show precisely how the verification engine can compute such non-provability information and how to build effective learning algorithms when invariants are expressed as Boolean combinations of a fixed set of predicates. Moreover, we evaluate our framework in two verification settings, one in which verification engines need to handle quantified formulas and one in which verification engines have to reason about heap properties expressed in an expressive but undecidable separation logic. Our experiments show that our invariant synthesis framework based on non-provability information can both effectively synthesize inductive invariants and adequately strengthen contracts across a large suite of programs

A catalogue of damped Lyman alpha absorption systems and radio flux densities of the background quasars

We present a catalogue of the 322 damped Lyman alpha absorbers taken from the literature. All damped Lyman alpha absorbers are included, with no selection on redshift or quasar magnitude. Of these, 123 are candidates and await confirmation using high resolution spectroscopy. For all 322 objects we catalogue the radio properties of the background quasars, where known. Around 60 quasars have radio flux densities above 0.1 Jy and approximately half of these have optical magnitudes brighter than V = 18. This compilation should prove useful in several areas of extragalactic/cosmological research.Comment: 26 Pages, 12 PS tables, 1 embedded table. Accepted by PASA. Continuously updated online catalogue available at http://www.phys.unsw.edu.au/~sjc/dl

Quantitative Phosphoproteomics of Proteasome Inhibition in Multiple Myeloma Cells

BACKGROUND: The proteasome inhibitor bortezomib represents an important advance in the treatment of multiple myeloma (MM). Bortezomib inhibits the activity of the 26S proteasome and induces cell death in a variety of tumor cells; however, the mechanism of cytotoxicity is not well understood. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the differential phosphoproteome upon proteasome inhibition by using stable isotope labeling by amino acids in cell culture (SILAC) in combination with phosphoprotein enrichment and LC-MS/MS analysis. In total 233 phosphoproteins were identified and 72 phosphoproteins showed a 1.5-fold or greater change upon bortezomib treatment. The phosphoproteins with expression alterations encompass all major protein classes, including a large number of nucleic acid binding proteins. Site-specific phosphopeptide quantitation revealed that Ser38 phosphorylation on stathmin increased upon bortezomib treatment, suggesting new mechanisms associated to bortezomib-induced apoptosis in MM cells. Further studies demonstrated that stathmin phosphorylation profile was modified in response to bortezomib treatment and the regulation of stathmin by phosphorylation at specific Ser/Thr residues participated in the cellular response induced by bortezomib. CONCLUSIONS/SIGNIFICANCE: Our systematic profiling of phosphorylation changes in response to bortezomib treatment not only advanced the global mechanistic understanding of the action of bortezomib on myeloma cells but also identified previously uncharacterized signaling proteins in myeloma cells

The GATA1s isoform is normally down-regulated during terminal haematopoietic differentiation and over-expression leads to failure to repress MYB, CCND2 and SKI during erythroid differentiation of K562 cells

Background: Although GATA1 is one of the most extensively studied haematopoietic transcription factors little is currently known about the physiological functions of its naturally occurring isoforms GATA1s and GATA1FL in humans—particularly whether the isoforms have distinct roles in different lineages and whether they have non-redundant roles in haematopoietic differentiation. As well as being of general interest to understanding of haematopoiesis, GATA1 isoform biology is important for children with Down syndrome associated acute megakaryoblastic leukaemia (DS-AMKL) where GATA1FL mutations are an essential driver for disease pathogenesis. <p/>Methods: Human primary cells and cell lines were analyzed using GATA1 isoform specific PCR. K562 cells expressing GATA1s or GATA1FL transgenes were used to model the effects of the two isoforms on in vitro haematopoietic differentiation. <p/>Results: We found no evidence for lineage specific use of GATA1 isoforms; however GATA1s transcripts, but not GATA1FL transcripts, are down-regulated during in vitro induction of terminal megakaryocytic and erythroid differentiation in the cell line K562. In addition, transgenic K562-GATA1s and K562-GATA1FL cells have distinct gene expression profiles both in steady state and during terminal erythroid differentiation, with GATA1s expression characterised by lack of repression of MYB, CCND2 and SKI. <p/>Conclusions: These findings support the theory that the GATA1s isoform plays a role in the maintenance of proliferative multipotent megakaryocyte-erythroid precursor cells and must be down-regulated prior to terminal differentiation. In addition our data suggest that SKI may be a potential therapeutic target for the treatment of children with DS-AMKL

Directional Radiation and Photodissociation Regions in Molecular Hydrogen Clouds

Some astrophysical observations of molecular hydrogen point to a broadening of the velocity distribution for molecules at excited rotational levels. This effect is observed in both Galactic and high redshift clouds. Analysis of H_2, HD, and CI absorption lines has revealed the broadening effect in the absorption system of QSO 1232+082 (z_{abs}=2.33771). We analyze line broadening mechanisms by considering in detail the transfer of ultraviolet radiation (in the resonance lines of the Lyman and Werner H_2 molecular bands) for various velocity distributions at excited rotational levels. The mechanism we suggest includes the saturation of the lines that populate excited rotational levels (radiative pumping) and manifests itself most clearly in the case of directional radiation in the medium. Based on the calculated structure of a molecular hydrogen cloud in rotational level populations, we have considered an additional mechanism that takes into account the presence of a photodissociation region. Note that disregarding the broadening effects we investigated can lead to a significant systematic error when the data are processed.Comment: 14 pages, 10 figure