Faster Algorithms For Vertex Partitioning Problems Parameterized by Clique-width

Many NP-hard problems, such as Dominating Set, are FPT parameterized by clique-width. For graphs of clique-width $k$ given with a $k$-expression, Dominating Set can be solved in $4^k n^{O(1)}$ time. However, no FPT algorithm is known for computing an optimal $k$-expression. For a graph of clique-width $k$, if we rely on known algorithms to compute a $(2^{3k}-1)$-expression via rank-width and then solving Dominating Set using the $(2^{3k}-1)$-expression, the above algorithm will only give a runtime of $4^{2^{3k}} n^{O(1)}$. There have been results which overcome this exponential jump; the best known algorithm can solve Dominating Set in time $2^{O(k^2)} n^{O(1)}$ by avoiding constructing a $k$-expression [Bui-Xuan, Telle, and Vatshelle. Fast dynamic programming for locally checkable vertex subset and vertex partitioning problems. Theoret. Comput. Sci., 2013. doi:10.1016/j.tcs.2013.01.009]. We improve this to $2^{O(k\log k)}n^{O(1)}$. Indeed, we show that for a graph of clique-width $k$, a large class of domination and partitioning problems (LC-VSP), including Dominating Set, can be solved in $2^{O(k\log{k})} n^{O(1)}$. Our main tool is a variant of rank-width using the rank of a $0$-$1$ matrix over the rational field instead of the binary field.Comment: 13 pages, 5 figure

Decision Making in Virtual Worlds: An Experimental Test of Altruism, Fairness and Presence

Virtual worlds are gaining in popularity and are proposed as a test laboratory for the real world. Inthese virtual worlds users act via their avatars and make decisions for them. In this paper, we analyzethe decision making in virtual worlds in an experiment conducted in a virtual world, as well as in thereal world over the internet, for the same set of subjects. For this purpose, we develop hypotheses fordecision making in the context of a classic economic experiment (the Dictator Game). We find similardecisions in the virtual and the real world with respect to sharing. Altruism has a significant influencein the real world setting but not in the virtual world; fairness is insignificant in both settings. Weidentify the feeling of presence in one’s avatar and potential satiation effects as factors that influencedecisions regarding the allocation of resources in the virtual world

Rearrangement of cluster structure during fission processes

Results of molecular dynamics simulations of fission reactions $Na_{10}^{2+} \to Na_7^+ + Na_3^+$ and $Na_{18}^{2+} \to 2 Na_9^+$ are presented. Dependence of the fission barriers on isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. Importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual separation of the daughter fragments begins and/or forming a "neck" between the separating fragments

Future Flooding Impacts on Transportation Infrastructure and Traffic Patterns Resulting from Climate Change

This study investigated potential impacts of climate change on travel disruption resulting from road closures in two urban watersheds in the Portland metropolitan area. We used ensemble climate change scenarios, a hydrologic model, stream channel survey, a hydraulic model, and a travel forecast model to develop an integrated impact assessment method. High-resolution climate change scenarios are based on the combinations of two emission scenarios and eight general circulation models. The Precipitation-Runoff Modeling System was calibrated and validated for the period 1988-2006, and simulated for determining the probability of floods from 2020-2049. We surveyed stream cross sections at five road crossings for stream channel geometry and determined floodwater surface elevations using the HEC-RAS model. Four of the surveyed bridges and roadways were lower in elevation than the current 100-year floodwater surface elevation, leading to relatively frequent nuisance flooding. These roadway flooding events will become more frequent under some climate change scenarios in the future, but climate change impacts will depend on local geomorphic conditions. While vehicle miles traveled were not significantly affected by road closure, vehicle-hours delay demonstrated a greater impact from road closures, increasing by 10 percent in the Fanno Creek area. Results indicate that any cost analysis is extremely sensitive to the occurrence of human fatalities or injuries and fairly insensitive to delay costs. In addition, this research presents a comprehensive classification of flooding costs, identifies preventative measures, and makes short- and long-term recommendations. Our research demonstrated the usefulness of the integration of top-down and bottom-up approaches in climate change impact assessment, and the need for spatially explicit modeling and participatory planning in flood management and transportation planning under increasing climate uncertainty

A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis*

Endoribonuclease E (RNase E) is a regulator of global gene expression in Escherichia coli and is the best studied member of the RNase E/G ribonuclease family. Homologues are present in other bacteria but the roles of plant RNase E/G-like proteins are not known. Arabidopsis thaliana contains a single nuclear gene (At2g04270) encoding a product with the conserved catalytic domain of RNase E/G-like proteins. At2g04270 and the adjacent At2g04280 gene form converging transcription units with a ∼40 base overlap at their 3’ ends. Several translation products were predicted from the analyses of At2g04270 cDNAs. An antibody raised against a recombinant A. thaliana RNase E/G-like protein recognized a 125 kDa protein band in purified chloroplast preparations fractionated by SDS-PAGE. The 125 kDa RNase E/G-like protein was detected in cotyledons, rosette and cauline leaves. T-DNA insertions in exon 6 or intron 11 of At2g04270 result in loss of the 125 kDa band or truncation to a 110 kDa band. Loss of At2g04270 function resulted in the arrest of chloroplast development, loss of autotrophic growth, and reduced plastid ribosomal, psbA and rbcL RNA levels. Homozygous mutant plants were pale-green, contained smaller plastids with fewer thylakoids and shorter granal stacks than wild-type chloroplasts, and required sucrose at all growth stages following germination right up to flowering and setting seeds. Recombinant A. thaliana RNase E/G-like proteins rescued an E. coli RNase E mutant and cleaved an rbcL RNA substrate. Expression of At2g04270 was highly correlated with genes encoding plastid polyribonucleotide phosphorylase, S1 RNA-binding, and CRS1/YhbY domain proteins

Inflation with Non-minimal Gravitational Couplings and Supergravity

We explore in the supergravity context the possibility that a Higgs scalar may drive inflation via a non-minimal coupling to gravity characterised by a large dimensionless coupling constant. We find that this scenario is not compatible with the MSSM, but that adding a singlet field (NMSSM, or a variant thereof) can very naturally give rise to slow-roll inflation. The inflaton is necessarily contained in the doublet Higgs sector and occurs in the D-flat direction of the two Higgs doublets.Comment: 13 pages, 1 figur

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete characterizations for the structures that can be designed using restricted alphabets. Under a classic four-letter alphabet, we provide a complete characterization of designable structures without unpaired bases. When unpaired bases are allowed, we provide partial characterizations for classes of designable/undesignable structures, and show that the class of designable structures is closed under the stutter operation. Membership of a given structure to any of the classes can be tested in linear time and, for positive instances, a solution can be found in linear time. Finally, we consider a structure-approximating version of the problem that allows to extend bands (helices) and, assuming that the input structure avoids two motifs, we provide a linear-time algorithm that produces a designable structure with at most twice more base pairs than the input structure.Comment: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. LNCS, 201

Tumor-Specific Expression and Detection of a CEST Reporter Gene

Purpose To develop an imaging tool that enables the detection of malignant tissue with enhanced specificity using the exquisite spatial resolution of MRI. Methods Two mammalian gene expression vectors were created for the expression of the lysine-rich protein (LRP) under the control of the cytomegalovirus (CMV) promoter and the progression elevated gene-3 promoter (PEG-3 promoter) for constitutive and tumor-specific expression of LRP, respectively. Using those vectors, stable cell lines of rat 9L glioma, 9LCMV-LRP and 9LPEG-LRP, were established and tested for CEST contrast in vitro and in vivo. Results 9LPEG-LRP cells showed increased CEST contrast compared with 9L cells in vitro. Both 9LCMV-LRP and 9LPEG-LRP cells were capable of generating tumors in the brains of mice, with a similar growth rate to tumors derived from wild-type 9L cells. An increase in CEST contrast was clearly visible in tumors derived from both 9LCMV-LRP and 9LPEG-LRP cells at 3.4 ppm. Conclusion The PEG-3 promoter:LRP system can be used as a cancer-specific, molecular-genetic imaging reporter system in vivo. Because of the ubiquity of MR imaging in clinical practice, sensors of this class can be used to translate molecular-genetic imaging rapidly