Structural parameterizations for boxicity

The boxicity of a graph $G$ is the least integer $d$ such that $G$ has an intersection model of axis-aligned $d$-dimensional boxes. Boxicity, the problem of deciding whether a given graph $G$ has boxicity at most $d$, is NP-complete for every fixed $d \ge 2$. We show that boxicity is fixed-parameter tractable when parameterized by the cluster vertex deletion number of the input graph. This generalizes the result of Adiga et al., that boxicity is fixed-parameter tractable in the vertex cover number. Moreover, we show that boxicity admits an additive $1$-approximation when parameterized by the pathwidth of the input graph. Finally, we provide evidence in favor of a conjecture of Adiga et al. that boxicity remains NP-complete when parameterized by the treewidth.Comment: 19 page

Spectra of some new graph operations and some new classes of integral graphs

In this paper, we define duplication corona, duplication neighborhood corona and duplication edge corona of two graphs. We compute their adjacency spectrum, Laplacian spectrum and signless Laplacian. As an application, our results enable us to construct infinitely many pairs of cospectral graphs and also integral graphs. Keywords: Duplication corona, Duplication edge corona, Duplication neighborhood corona, Cospectral graphs, Integral graphs

Expanding the expressive power of Monadic Second-Order logic on restricted graph classes

We combine integer linear programming and recent advances in Monadic Second-Order model checking to obtain two new algorithmic meta-theorems for graphs of bounded vertex-cover. The first shows that cardMSO1, an extension of the well-known Monadic Second-Order logic by the addition of cardinality constraints, can be solved in FPT time parameterized by vertex cover. The second meta-theorem shows that the MSO partitioning problems introduced by Rao can also be solved in FPT time with the same parameter. The significance of our contribution stems from the fact that these formalisms can describe problems which are W[1]-hard and even NP-hard on graphs of bounded tree-width. Additionally, our algorithms have only an elementary dependence on the parameter and formula. We also show that both results are easily extended from vertex cover to neighborhood diversity.Comment: Accepted for IWOCA 201

A multinuclear NMR and quantum chemical study of solid trimethylammonium chloride

The solid salt, trimethylammonium chloride (TMAC), is investigated by a combination of NMR spectroscopic techniques and quantum chemical calculations. Chemical shift and nuclear quadrupolar interaction parameters have been measured for 35Cl, 1H/2H, and 15N/14N. These parameters have also been calculated as a function of the hydrogen position in the N\u2022\u2022\u2022H\u2022\u2022\u2022Cl fragment. Overall, the measured parameters are consistent with a structure in which the hydrogen is completely transferred to the nitrogen (i.e., N\u2013H\u2022\u2022\u2022Cl). The high hydrogen chemical shift (10.9 ppm by 2H CP/MAS) and relatively small deuterium quadrupolar coupling constant (127 kHz) indicate a moderately strong N\u2013H\u2022\u2022\u2022Cl hydrogen bond. A pronounced deuterium isotope effect on the 35Cl quadrupolar coupling constant is observed.Peer reviewed: YesNRC publication: Ye

When the optimal is not the best: parameter estimation in complex biological models

Background: The vast computational resources that became available during the past decade enabled the development and simulation of increasingly complex mathematical models of cancer growth. These models typically involve many free parameters whose determination is a substantial obstacle to model development. Direct measurement of biochemical parameters in vivo is often difficult and sometimes impracticable, while fitting them under data-poor conditions may result in biologically implausible values. Results: We discuss different methodological approaches to estimate parameters in complex biological models. We make use of the high computational power of the Blue Gene technology to perform an extensive study of the parameter space in a model of avascular tumor growth. We explicitly show that the landscape of the cost function used to optimize the model to the data has a very rugged surface in parameter space. This cost function has many local minima with unrealistic solutions, including the global minimum corresponding to the best fit. Conclusions: The case studied in this paper shows one example in which model parameters that optimally fit the data are not necessarily the best ones from a biological point of view. To avoid force-fitting a model to a dataset, we propose that the best model parameters should be found by choosing, among suboptimal parameters, those that match criteria other than the ones used to fit the model. We also conclude that the model, data and optimization approach form a new complex system, and point to the need of a theory that addresses this problem more generally

Characterization and hormonal modulation of immunoreactive thiamin carrier protein secreted by adult rat Leydig cells in vitro

Leydig cells isolated from adult rats and maintained under defined conditions in culture secrete a protein of molecular weight (Mr) 70 000 which is immunologically similar to chicken thiamin carrier protein (TCP). Synthesis of immunoreactive TCP by these cells is demonstrated by immunoprecipitation of [35S]methionine incorporated, newly synthesized proteins with monoclonal and polyclonal antibodies to chicken TCP. The amount of immunoreactive TCP secreted into the culture supernatant is quantitated by using a specific radioimmunoassay. Under the influence of LH, secretion of immunoreactive TCP is enhanced 3-fold and can be inhibited by up to 70% with aromatase inhibitor (1,4,6-androstatrien-3,17-dione). Cyclic AMP acts as a second messenger in the sequence of events involved in LH-induced elevation of immunoreactive TCP in Leydig cells. The effects of exogenous estradiol-17beta and diethylstilbestrol are comparable in terms of stimulation of secretion of immunoreactive TCP by these cells. Tamoxifen brought about a 70% decrease in the elevated levels of immunoreactive TCP. These results suggest that estrogen mediates immunoreactive TCP induction in hormonally stimulated adult rat Leydig cells

Diamine oxidase of Lathyrus sativus seedlings. Purification and properties

Diamine oxidase (EC 1.4.3.6) was purified from 5-day-old etiolated seedlings of Lathyrus sativus by MnCl2 treatment, (NH4)2SO4 and acetone fractionations, DEAE-Sephadex chromatography followed by gel filtration on Sephadex G-200. A single step purification of the enzyme was achieved by using an immunoaffinity column, wherein rabbit antibodies to the homogeneous diamine oxidase were coupled to CNBr-activated Sepharose. The enzyme thus obtained was homogeneous by electrophoretic, immunological and ultracentrifugal criteria. It had an Mr of 148,000 (6.46S) and was a dimer with similar sub-units (Mr 75,000). Amino acid analysis showed the absence of cysteine residues although it contained five disulphide bonds. The enzyme had copper (2.7 g atom/mol enzyme) but was not a glycoprotein. No absorption maximum in the visible region was detectable. Ethylenediamine 1,3-diaminopropane and histamine were potent competitive inhibitors for the substrate putrescine. The addition of monospecific antibodies to the enzyme increased the Km for benzyl amine without any change in the Vmax Diamine oxidase from pea seedling, partially purified, exhibited complete crossreactivity with the antibodies to the L. sativus enzyme

Arginine decarboxylase is a component activity of the multifunctional enzyme putrescine synthase in cucumber seedlings

A homogenous PreParation of Putrescine synthase, the versatile multifunctional enzyme involved in agmatine →Putrescine conversion inCucumis sativus was found to catalyze enzymatic decarboxylation of arginine also. Similarly, the Purified arginine decarboxylase mediated the comPonent as well as the comPlete set of couPled reactions harboured by Putrescine synthase. Both the enzyme PreParations exhibited identical electroPhoretic and chromatograPhic behaviour and were immunologically indistinguishable. All the enzymic activities are stabilized concurrently by feeding arginine to the intact seedlings. Therefore, it is concluded that the multifunctional Putrescine synthase inCucumis sativus seedlings also harbours arginine decarboxylase activity unlike its counterPart in Lathyrus sativus

Purification and characterization of arginine decarboxylase from cucumber (Cucumis sativus) seedlings

A simple, reproducible and rapid protocol for the purification of arginine decarboxylase fromCucumis sativus seedlings has been standardised. The purification steps involved ion-exchange chromatography on diethylaminoethyl-cellulose followed by gel filtration on Sephadex G-l 50. The purified enzyme preparation migrated as a single stainable band on Polyacrylamide gels at both basic and acidic pH, but under denaturing and reducing conditions on sodium dodecyl sulphate-polyacrylamide gels resolved into polypeptides of molecular weight 48,000,44,000 and 15,000. However, in the absence of 2-mercaptoethanol on electrophoresis on sodium dodecyl sulphate-polyacrylamide gels, the enzyme moved as single band with a molecular weight of 150,000. Evidence was obtained to indicate that these three polypeptides were probably derived from a single larger molecular weight enzyme. On storage of the purified protein, the 48,000 species was preferentially degraded to smaller polypeptides. The preliminary data suggested that the 48,000 and 44,000 species shared many common tryptic peptides as revealed by finger printing of the [125I ]-labelled protein. The purified enzyme was a glycoprotein and had a Km of 0.5 mM for arginine. Its activity was stimulated by dithiothrietol and pyridoxal phosphate. EDTA did not inhibit the enzyme activity. Mn2+ at 1 mM stimulated arginine decarboxylase activity but was inhibitory at higher concentration

Biosynthesis and regulation of polyamines in higher plants

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