A New Lower Bound on the Maximum Number of Satisfied Clauses in Max-SAT and its Algorithmic Applications

A pair of unit clauses is called conflicting if it is of the form $(x)$, $(\bar{x})$. A CNF formula is unit-conflict free (UCF) if it contains no pair of conflicting unit clauses. Lieberherr and Specker (J. ACM 28, 1981) showed that for each UCF CNF formula with $m$ clauses we can simultaneously satisfy at least \pp m clauses, where \pp =(\sqrt{5}-1)/2. We improve the Lieberherr-Specker bound by showing that for each UCF CNF formula $F$ with $m$ clauses we can find, in polynomial time, a subformula $F'$ with $m'$ clauses such that we can simultaneously satisfy at least \pp m+(1-\pp)m'+(2-3\pp)n"/2 clauses (in $F$), where $n"$ is the number of variables in $F$ which are not in $F'$. We consider two parameterized versions of MAX-SAT, where the parameter is the number of satisfied clauses above the bounds $m/2$ and $m(\sqrt{5}-1)/2$. The former bound is tight for general formulas, and the later is tight for UCF formulas. Mahajan and Raman (J. Algorithms 31, 1999) showed that every instance of the first parameterized problem can be transformed, in polynomial time, into an equivalent one with at most $6k+3$ variables and $10k$ clauses. We improve this to $4k$ variables and $(2\sqrt{5}+4)k$ clauses. Mahajan and Raman conjectured that the second parameterized problem is fixed-parameter tractable (FPT). We show that the problem is indeed FPT by describing a polynomial-time algorithm that transforms any problem instance into an equivalent one with at most $(7+3\sqrt{5})k$ variables. Our results are obtained using our improvement of the Lieberherr-Specker bound above

Aluminum action on mouse bone cell metabolism and response to PTH and 1,25(OH)2D3

Aluminum action on mouse bone cell metabolism and response to PTH and 1,25(OH)2D3. Aluminum (Al) accumulation in bone is associated with low bone formation and mineralization rates; resorption may also be reduced. The mechanism of these Al-induced changes was investigated using cultured mouse osteoblast–like (OB) and osteoclast–like (OC) cells. The Al effect on bone resorption was measured by the in vitro release of 45Ca and β-glucuronidase from mouse fetal limb–bones. Al had a biphasic effect. High concentrations (>1.5 × 10-6 M) of Al inhibited collagen and DNA synthesis, ornithine decarboxylase and alkaline phosphatase activity in OB, and depressed tartrate-resistant acid phosphatase activity in OC. Lower Al concentrations stimulated these cellular activities and 45Ca and β-glucuronidase release from fetal bones. Al had no effect on basal cAMP levels in OB but inhibited the stimulating effect of bPTH on cAMP content. Al also altered the 1,25(OH)2D3 effects on the ornithine decarboxylase activity of OB cells. These data suggest that: (i) the low bone formation observed in vivo during Al intoxication may be due to the inhibition of collagen synthesis and to depressed cell proliferation; and (ii) Al may indirectly influence bone remodeling by interfering with the actions of bPTH and 1,25(OH)2D3 on bone cells

Modelling Small-Scale Drifting Snow with a Lagrangian Stochastic Model Based on Large-Eddy Simulations

Observations of drifting snow on small scales have shown that, in spite of nearly steady winds, the snow mass flux can strongly fluctuate in time and space. Most drifting snow models, however, are not able to describe drifting snow accurately over short time periods or on small spatial scales as they rely on mean flow fields and assume equilibrium saltation. In an attempt to gain understanding of the temporal and spatial variability of drifting snow on small scales, we propose to use a model combination of flow fields from large-eddy simulations (LES) and a Lagrangian stochastic model to calculate snow particle trajectories and so infer snow mass fluxes. Model results show that, if particle aerodynamic entrainment is driven by the shear stress retrieved from the LES, we can obtain a snow mass flux varying in space and time. The obtained fluctuating snow mass flux is qualitatively compared to field and wind-tunnel measurements. The comparison shows that the model results capture the intermittent behaviour of observed drifting snow mass flux yet differences between modelled turbulent structures and those likely to be found in the field complicate quantitative comparisons. Results of a model experiment show that the surface shear-stress distribution and its influence on aerodynamic entrainment appear to be key factors in explaining the intermittency of drifting snow

Synthesizing Iterators from Abstraction Functions

A technique for synthesizing iterators from declarative abstraction functions written in a relational logic specification language is described. The logic includes a transitive closure operator that makes it convenient for expressing reachability queries on linked data structures. Some optimizations, including tuple elimination, iterator flattening, and traversal state reduction, are used to improve performance of the generated iterators. A case study demonstrates that most of the iterators in the widely used JDK Collections classes can be replaced with code synthesized from declarative abstraction functions. These synthesized iterators perform competitively with the hand-written originals. In a user study the synthesized iterators always passed more test cases than the hand-written ones, were almost always as efficient, usually took less programmer effort, and were the qualitative preference of all participants who provided free-form comments

Scrap your boilerplate with object algebras

International audienceTraversing complex Abstract Syntax Trees (ASTs) typically requires large amounts of tedious boilerplate code. For many operations most of the code simply walks the structure, and only a small portion of the code implements the functional- ity that motivated the traversal in the first place. This paper presents a type-safe Java framework called Shy that removes much of this boilerplate code. In Shy Object Algebras are used to describe complex and extensible AST structures. Using Java annotations Shy generates generic boilerplate code for various types of traversals. For a concrete traversal, users of Shy can then inherit from the generated code and over- ride only the interesting cases. Consequently, the amount of code that users need to write is significantly smaller. Moreover, traversals using the Shy framework are also much more structure shy, becoming more adaptive to future changes or extensions to the AST structure. To prove the effectiveness of the approach, we applied Shy in the implementation of a domain-specific questionnaire language. Our results show that for a large number of traversals there was a significant reduction in the amount of user-defined code

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase

UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the ‘Dicty annotation marathon’, a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set

Designing an automatic pollen monitoring network for direct usage of observations to reconstruct the concentration fields

We consider several approaches to a design of a regional-to-continent-scale automatic pollen monitoring network in Europe. Practical challenges related to the arrangement of such a network limit the range of possible solutions. A hierarchical network is discussed, highlighting the necessity of a few reference sites that follow an extended observations protocol and have corresponding capabilities. Several theoretically rigorous approaches to a network design have been developed so far. However, before starting the process, a network purpose, a criterion of its performance, and a concept of the data usage should be formalized. For atmospheric composition monitoring, developments follow one of the two concepts: a network for direct representation of concentration fields and a network for model-based data assimilation, inverse problem solution, and forecasting. The current paper demonstrates the first approach, whereas the inverse problems are considered in a follow-up paper. We discuss the approaches for the network design from theoretical and practical standpoints, formulate criteria for the network optimality, and consider practical constraints for an automatic pollen network. An application of the methodology is demonstrated for a prominent example of Germany's pollen monitoring network. The multi-step method includes (i) the network representativeness and (ii) redundancy evaluation followed by (iii) fidelity evaluation and improvement using synthetic data