310 research outputs found
Fast Dynamic Graph Algorithms for Parameterized Problems
Fully dynamic graph is a data structure that (1) supports edge insertions and
deletions and (2) answers problem specific queries. The time complexity of (1)
and (2) are referred to as the update time and the query time respectively.
There are many researches on dynamic graphs whose update time and query time
are , that is, sublinear in the graph size. However, almost all such
researches are for problems in P. In this paper, we investigate dynamic graphs
for NP-hard problems exploiting the notion of fixed parameter tractability
(FPT).
We give dynamic graphs for Vertex Cover and Cluster Vertex Deletion
parameterized by the solution size . These dynamic graphs achieve almost the
best possible update time and the query time
, where is the time complexity of any static
graph algorithm for the problems. We obtain these results by dynamically
maintaining an approximate solution which can be used to construct a small
problem kernel. Exploiting the dynamic graph for Cluster Vertex Deletion, as a
corollary, we obtain a quasilinear-time (polynomial) kernelization algorithm
for Cluster Vertex Deletion. Until now, only quadratic time kernelization
algorithms are known for this problem.
We also give a dynamic graph for Chromatic Number parameterized by the
solution size of Cluster Vertex Deletion, and a dynamic graph for
bounded-degree Feedback Vertex Set parameterized by the solution size. Assuming
the parameter is a constant, each dynamic graph can be updated in
time and can compute a solution in time. These results are obtained by
another approach.Comment: SWAT 2014 to appea
Possibilities of alternative generation II biotests at Artemia
The meaning of alternative biotests is described and discussed. The paper also deals with the possible application of the developmental studies of the sea Artemia franciscana nauplinus. Five-day biotests including the validation criteria are described. The possibilities of the biotests are very wide. Additionally to the standard applications in ecotoxicology, there is a possibility of modelling pharmacological experiments or monitoring the effects of ionizing radiation and the interaction with other chemicals
Fluorescence (TALIF) measurement of atomic hydrogen concentration in a coplanar surface dielectric barrier discharge
Spatially and temporally resolved measurements of atomic hydrogen concentration above the dielectric of coplanar barrier discharge are presented for atmospheric pressure in 2.2% H2/Ar. The measurements were carried out in the afterglow phase by means of two-photon absorption laser-induced fluorescence (TALIF). The difficulties of employing the TALIF technique in close proximity to the dielectric surface wall were successfully addressed by taking measurements on a suitable convexly curved dielectric barrier, and by proper mathematical treatment of parasitic signals from laser–surface interactions. It was found that the maximum atomic hydrogen concentration is situated closest to the dielectric wall from which it gradually decays. The maximum absolute concentration was more than 10^22 m-3. In the afterglow phase, the concentration of atomic hydrogen above the dielectric surface stays constant for a considerable time (10 us - 1 ms), with longer times for areas situated farther from the dielectric surface. The existence of such a temporal plateau was explained by the presented 1D model: the recombination losses of atomic hydrogen farther from the dielectric surface are compensated by the diffusion of atomic hydrogen from regions close to the dielectric surface. The fact that a temporal plateau exists even closest to the dielectric surface suggests that the dielectric surface acts as a source of atomic hydrogen in the afterglow phase
Preprocessing Argumentation Frameworks via Replacement Patterns
A fast-growing research direction in the study of formal argumentation is the development of practical systems for central reasoning problems underlying argumentation. In particular, numerous systems for abstract argumentation frameworks (AF solvers) are available today, covering several argumentation semantics and reasoning tasks. Instead of proposing another algorithmic approach for AF solving, we introduce in this paper distinct AF preprocessing techniques as a solver-independent approach to obtaining performance improvements of AF solvers. We establish a formal framework of replacement patterns to perform local simplifications that are faithful with respect to standard semantics for AFs. Moreover, we provide a collection of concrete replacement patterns. Towards potential applicability, we employ the patterns in a preliminary empirical evaluation of their influence on AF solver performance.Peer reviewe
Lattice models and Landau theory for type II incommensurate crystals
Ground state properties and phonon dispersion curves of a classical linear
chain model describing a crystal with an incommensurate phase are studied. This
model is the DIFFOUR (discrete frustrated phi4) model with an extra
fourth-order term added to it. The incommensurability in these models may arise
if there is frustration between nearest-neighbor and next-nearest-neighbor
interactions. We discuss the effect of the additional term on the phonon
branches and phase diagram of the DIFFOUR model. We find some features not
present in the DIFFOUR model such as the renormalization of the
nearest-neighbor coupling. Furthermore the ratio between the slopes of the soft
phonon mode in the ferroelectric and paraelectric phase can take on values
different from -2. Temperature dependences of the parameters in the model are
different above and below the paraelectric transition, in contrast with the
assumptions made in Landau theory. In the continuum limit this model reduces to
the Landau free energy expansion for type II incommensurate crystals and it can
be seen as the lowest-order generalization of the simplest Lifshitz-point
model. Part of the numerical calculations have been done by an adaption of the
Effective Potential Method, orginally used for models with nearest-neighbor
interaction, to models with also next-nearest-neighbor interactions.Comment: 33 pages, 7 figures, RevTex, submitted to Phys. Rev.
Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat 3 wild emmer wheat RIL population
Mineral nutrient malnutrition, and particularly
deficiency in zinc and iron, afflicts over 3 billion people
worldwide. Wild emmer wheat, Triticum turgidum ssp.
dicoccoides, genepool harbors a rich allelic repertoire for
mineral nutrients in the grain. The genetic and physiological
basis of grain protein, micronutrients (zinc, iron,
copper and manganese) and macronutrients (calcium,
magnesium, potassium, phosphorus and sulfur) concentration
was studied in tetraploid wheat population of 152
recombinant inbred lines (RILs), derived from a cross
between durum wheat (cv. Langdon) and wild emmer
(accession G18-16). Wide genetic variation was found
among the RILs for all grain minerals, with considerable
transgressive effect. A total of 82 QTLs were mapped for
10 minerals with LOD score range of 3.2–16.7. Most QTLs
were in favor of the wild allele (50 QTLs). Fourteen pairs
of QTLs for the same trait were mapped to seemingly
homoeologous positions, reflecting synteny between the A
and B genomes. Significant positive correlation was found
between grain protein concentration (GPC), Zn, Fe and Cu,
which was supported by significant overlap between the
respective QTLs, suggesting common physiological and/or
genetic factors controlling the concentrations of these
mineral nutrients. Few genomic regions (chromosomes 2A,
5A, 6B and 7A) were found to harbor clusters of QTLs for
GPC and other nutrients. These identified QTLs may
facilitate the use of wild alleles for improving grain
nutritional quality of elite wheat cultivars, especially in
terms of protein, Zn and Fe
SmCL3, a Gastrodermal Cysteine Protease of the Human Blood Fluke Schistosoma mansoni
Parasitic infection caused by blood flukes of the genus Schistosoma is a major global health problem. More than 200 million people are infected. Identifying and characterizing the constituent enzymes of the parasite's biochemical pathways should reveal opportunities for developing new therapies (i.e., vaccines, drugs). Schistosomes feed on host blood, and a number of proteolytic enzymes (proteases) contribute to this process. We have identified and characterized a new protease, SmCL3 (for Schistosoma mansoni cathepsin L3), that is found within the gut tissue of the parasite. We have employed various biochemical and molecular biological methods and sequence similarity analyses to characterize SmCL3 and obtain insights into its possible functions in the parasite, as well as its evolutionary position among cathepsin L proteases in general. SmCL3 hydrolyzes major host blood proteins (serum albumin and hemoglobin) and is expressed in parasite life stages infecting the mammalian host. Enzyme substrate specificity detected by positional scanning-synthetic combinatorial library was confirmed by molecular modeling. A sequence analysis placed SmCL3 to the cluster of other cathepsins L in accordance with previous phylogenetic analyses
RNA Interference in Schistosoma mansoni Schistosomula: Selectivity, Sensitivity and Operation for Larger-Scale Screening
RNA interference (RNAi) is a technique to selectively suppress mRNA of individual genes and, consequently, their cognate proteins. RNAi using double-stranded (ds) RNA has been used to interrogate the function of mainly single genes in the flatworm, Schistosoma mansoni, one of a number of schistosome species causing schistosomiasis. In consideration of large-scale screens to identify candidate drug targets, we examined the selectivity and sensitivity (the degree of suppression) of RNAi for 11 genes produced in different tissues of the parasite: the gut, tegument (surface) and otherwise. We used the schistosomulum stage prepared from infective cercariae larvae which are accessible in large numbers and adaptable to automated screening platforms. We found that RNAi suppresses transcripts selectively, however, the sensitivity of suppression varies (40%–>75%). No obvious changes in the parasite occurred post-RNAi, including after targeting the mRNA of genes that had been computationally predicted to be essential for survival. Additionally, we defined operational parameters to facilitate large-scale RNAi, including choice of culture medium, transfection strategy to deliver dsRNA, dose- and time-dependency, and dosing limits. Finally, using fluorescent probes, we show that the developing gut allows rapid entrance of dsRNA into the parasite to initiate RNAi
Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis
A total of 944 expressed sequence tags (ESTs) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat (Triticum aestivum L.). EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and 1D with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences (E ≤ e(−10)), where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses
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