bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monte Carlo and Markov Chain techniques for network reliability and sampling
Authors: Buchsbaum Adam L. , Mihail Milena 
Published: May 2007

AbstractWe examine a heuristic to approximate various reliability‐related parameters of communications networks under link failures. The heuristic is based on Monte Carlo and Markov chain simulation techniques. (These techniques have emerged in recent years in theoretical computer science in the context of obtaining efficient approximations forNP‐hard combinatorial optimization problems.) We present the ideas of these Monte Carlo and Markov chain techniques in terms of a specific reliability measure. The general method could be applicable to other reliability measures, just as it has been applied to other combinatorial problems. We present initial experimental results that suggest our approach is typically efficient in the computational complexity sense (running in time polynomial the size of the input); furthermore, our results suggest practical applicability for medium‐size networks and single‐edge parameters. As an example, we present the results of our experiments on a network that was posed for analysis by Applied Research at Bellcore: We estimated all single‐edge parameters on a single DEC‐5000 in less than 4 hours. The software that supported our experiments involves approximately 3000 lines of C code and is easy to adapt to other applications.
A forbidden minor characterization and reliability of a class of partial 4‐trees
Authors: Lingner Gerard T. , Politof Themistocles , Satyanarayana A. 
Published: May 2007

AbstractThis paper characterizes a class 𝒢 of partial 4‐trees in terms of a set of seven forbidden minors. The class 𝒢 contains several known classes of graphs, including both Δ ‐ Y and Y ‐ Δ graphs. A set of six graph reduction operations is defined, and it is shown that a graph G ∈ 𝒢 iff G can be reduced to an edgeless graph by a finite sequence of these operations. The all‐terminal reliability R(G) of a graph G is the probability that G is connected. The characterization of 𝒢 is used to develop an O(n log n) algorithm to compute R(G) for all n‐point graphs in 𝒢. The running time is O(n) for planar graphs in 𝒢.
Consecutive cuts and paths, and bounds onk‐terminal reliability
Authors: Strayer Heidi J. , Colbourn Charles J. 
Published: May 2007

AbstractShanthikumar developed an upper bound for two‐terminal reliability based on consecutives – tcutsets. Subsequently, Shier generalized this strategy to obtain upper bounds from cutsets, and lower bounds from pathsets, when the cutsets or pathsets form a semilattice structure. We examine a restricted case of Shier's method that yields ak‐terminal lower bound based on consecutive pathsets. Our approach employs a common reduction of consecutive cut and path bounds to the computation of the two‐terminal reliability of an interval graph with imperfect vertices. Computational results are given to support the observation that the consecutive paths lower bound is competitive with the best efficiently computable bounds that are currently available. We then apply the consecutive path bound to reduce, in some cases dramatically, the number of states generated in a most probable state bounding method.
An adaptive discretization algorithm for a class of continuous network programs
Authors: Philpott Andrew B. , Craddock Mark 
Published: May 2007

AbstractAn algorithm is derived for a class of continuous‐time minimum‐cost network flow problems. The algorithm is based on some recent results in the theory of separated continuous linear programs and works with a sequence of discrete approximations to the continuous‐time problem. We prove the convergence of the algorithm and present some numerical results which compare its performance against that of linear network flow algorithms applied to a uniform discrete approximation of the continuous‐time problem.
Projected dynamical systems modeling and computation of spatial network equilibria
Authors: Nagurney Anna , Takayama Takashi , Zhang Ding 
Published: May 2007

AbstractIn this paper, we consider the price formulation—rather than the quantity formulation—of spatial network equilibria and introduce a projected dynamical system, whose set of stationary points corresponds to the set of solutions of the governing variational inequality problem. We then interpret the dynamical system as a tatonnement process in which the commodity prices and shipments are updated simultaneously. We propose an Euler‐type method for the computation of the commodity prices and trade patterns, provide convergence results, and demonstrate that the algorithm can be implemented on massively parallel architectures. The notable feature of the algorithm is that the prices and shipments can be computed independently and in closed form. Finally, we illustrate the performance of the implemented algorithm on the Thinking Machine's CM‐2 and CM‐5 architectures.
The helical cube network
Authors: Somani Arun K. , Thatte Sanjay 
Published: May 2007

AbstractThe binary cube is a popular interconnection structure due to its desirable properties such as symmetry, regularity, low diameter, and high fault‐tolerance characteristics. The biggest drawback of this structure, however, is that the number of nodes in this structure grows only as an integer power of two. To remove this deficiency, a number of alternatives have been suggested, each with some limitations. in this paper, we introduce a variation of this interconnection structure called the helical cube. The proposed structure withKnodes strives to preserve all desirable properties of the binary cube such as regularity, simplicity of routing, and fault tolerance (connectivity of the graph). It removes the restriction on the number of nodes being a power of two while maintaining connectivityc, where ⌊logK⌋ ≤c≤ ⌈logK⌉. The degree of each node remains either ⌈logK⌉ or ⌊logK⌋ depending on the location of a node and total number of nodes in the structure.
Bipartite regular graphs with fixed diameter
Authors: Broersma H. J. , Göbel F. 
Published: May 2007

AbstractFor given nonnegative integers k and D, we consider the problem of determining n0(k, D), The smallest number n for which there exists a k‐regular bipartite graph on n vertices with diameter D. We solve the problem for all pairs (k, D) with D ≢ 2 (mod 4) and D ≢ 3 (mod 4), for all pairs (k, D) with k even or k prime and D ≢ 3 (mod 4), for all pairs with D ≤ 9 or k ≤ 4, and for a few other pairs. in the remaining cases, we obtain lower and upper bounds for n0(k, D).
On the generalized minimum spanning tree problem
Authors: Myung Young‐Soo , Lee Chang‐Ho , Tcha Dong‐Wan 
Published: May 2007

AbstractThis paper considers the Generalized Minimum Spanning Tree Problem (GMSTP). Given an undirected graph whose nodes are partitioned into mutually exclusive and exhaustive node sets, The GMSTP is then to find a minimum‐cost tree which includes exactly one node from each node set. Here, we show that the GMSTP is NP‐hard and that unless P = NP no polynomial‐time heuristic algorithm with a finite worst‐case performance ratio can exist for the GMSTP. We present various integer programming formulations for the problem and compare their linear programming relaxations. Based on the tightest formulation among the ones proposed, a dual‐based solution procedure is developed and shown to be efficient from computing experiments.
Computing the 2‐median on tree networks in O(n lg n) time
Authors: Gavish Bezalel , Sridhar Suresh 
Published: May 2007

AbstractLocation of facilities on tree networks is an important problem in transportation and telecommunication systems. For tree networks, The best‐known algorithm to find 2‐medians has a time complexity of O(n2). By exploiting the properties relating the 1‐median and the 2‐medians in tree networks, and the properties inherent in tree structure, an improved algorithm is developed for computing the 2‐median. The time complexity of this algorithm is O(n lg n). The details of the algorithm are described along with an illustrative example.
Betrachtungen über die Planetenbewegung
Authors: Mohr† O. 
Published: May 2007

AbstractIm Nachlasse des am 2. Oktober 1918 verstorbenen Vertreters der technischen Mechanik an der Dresdener Hochschule fand sich der folgende, aus seiner letzten Lebenszeit stammende Aufsatz. Wenn Dieser auch seinem mehr didaktischen Inhalt nach sich dem Rahmen der Zeitschrift nur schwer einfügt, so glaubte die Schriftleitung doch, mit der VeröffeNtlichung einer Ehrenpflicht gegenüber dem um die Wissenschaft hochverdienten Forscher genügen zu sollen.
Synthesis of the structured lipid 1,3‐dioleoyl‐2‐palmitoylglycerol from palm oil
Authors: Chen Ming‐Lung , Vali Shaik Ramjan , Lin Jih‐Yao , Ju Yi‐Hsu 
Published: May 2007

AbstractHuman milk fat contains 20–25% palmitic acid (16∶0) and 30–35% oleic acid (18∶1). More than 60% of the plamitic acid occurs at the sn‐2 position of the glycerol backbone. Palm oil is a rich source of both palmitic and oleic acids. The structured lipid 1,3‐dioleyl‐2‐palmitoylglycerol (OPO) is an important ingredient in infant formula. OPO was synthesized from palm oil by a three‐step method. In the first step, low‐temperature fractionation was applied to palm oil FA, yielding a palmitic acid‐rich fraction (87.8%) and an oleic acid‐rich fraction (96%). The palmitic acid content was further increased to 98.3% by transforming palmitic acid into ethyl palmitate. In the second step, esterification of ethyl palmitate and glycerol catalyzed by lipase Novozym 435 under vacuum (40 mm Hg) was employed for the synthesis of tripalmitin. Finally, OPO was obtained by the reaction of tripalmitin. Finally, OPO was obtained by the reaction of tripalmitin with oleic acid catalyzed by Lipase IM 60. In this final step, the TAG content in the product acylglycerol mixture was 97%, and 66.1% oleic acid was incorporated into TAG. Analysis of the FA composition at the sn‐2 position of TAG showed 90.7 mol% of palmitic acid and 9.3 mol% of oleic acid. OPO content in the product TAG was ca. 74 mol%. Thus, an efficient method was developed for the synthesis of OPO from palm oil.
Enzymatic pretreatment on rose‐hip oil extraction: Hydrolysis and pressing conditions
Authors: Concha J. , Soto C. , Chamy R. , Zúñiga M. E. 
Published: May 2007

AbstractIn a previous report [Zúñiga, M.E., J. Concha, C. Soto, and R. Chamy, Effect of the Rose Hip (Rosa aff. rubiginosa) Oil Extraction Cold‐Pressed Process, in Proceedings of the World Conference and Exhibition on Oilseed Processing, and Utilization, edited by R.F. Wilson, AOCS Press, Champaign, 2001, pp. 210–213], the authors showed that an enzymatic pretreatment of rose‐hip seeds, prior to oil extraction by cold pressing, improves the oil yield. In this work, we studied the effects of temperature and moisture during the enzymatic hydrolysis stage using two previously selected mixtures of commercial enzymes: (i) Olivex (mainly pectinase) plus Cellubrix (mainly cellulase), and (ii) Finizym (mainly β‐glucanase) plus Cellubrix (mainly cellulase) (all from Novozymes A/S, Madrid, Spain). In addition, we evaluated the effect of enzymatic hydrolysis on the oil extraction pressing rate at different operational pressures. Samples hydrolyzed enzymatically by either of the two commercial enzyme mixtures at 45°C and 30–40% moisture showed oil extraction yields up to 60%, an increase of greater than 50%, as compared with control samples in which the enzyme solutions were replaced by water. Both the oil extraction rate and yield by pressing increased when enzymatic pretreatment was applied. The oil extraction yield increased slightly when the operation pressure was elevated; however, when the sample was preheated, the oil extraction yield was greatly increased, especially for enzyme‐treated samples. Results confirmed the importance of temperature and moisture as enzymatic hydrolysis parameters that improve rose‐hip oil extraction yields in the cold‐pressing process. When pressing was carried out after preheating enzymatically treated samples, it was possible to increase the oil extraction yield to 72% compared with the control without preheating, which resulted in a 46% oil yield.
An enzymatic method for the synthesis of mixed‐acid phosphatidylcholine
Authors: Adlercreutz Dietlind , Wehtje Ernst 
Published: May 2007

AbstractThe enzymatic synthesis of PC with decanoic acid in the sn‐1 and hexanoic acid in the sn‐2 position is described. The procedure comprises the following enzymatic steps: (i) treatment of egg yolk with phospholipase A2 (PLA2) to hydrolyze egg yolk PC to 1‐acyl lysophosphatidylcholine (LPC); (ii) esterification of 1‐acyl LPC with hexanoic acid catalyzed by PLA2 to yield PC with hexanoic acid in the sn‐2 position; (iii) removal of the FA in the sn‐1 position by lipase‐catalyzed ethanolysis to yield 2‐hexanoyl LPC; and finally (iv) introduction of decanoic acid in this position by lipase‐catalyzed esterification of 2‐hexanoyl LPC to yield 1‐decanoyl‐2‐hexanoyl‐PC. Two egg yolks with a weight of 16 g were required to obtain 160 mg of the desired product. The chemical purity of the PC product and the positional purity of the FA were around 99%. The method is applicable for the synthesis of other mixed‐acid PC species as well.
Preparation of laurel oil alkanolamide from laurel oil
Authors: Kolancilar Hakan 
Published: May 2007

AbstractA low‐temperature synthesis of laurel oil alkanolamides directly from laurel oil and ethanolamine was carried out in essentially quantitative yields. The ethanolamine/laurel oil molar ratio used was 10∶1. Even though amine served as a catalyst in the reaction, we used sodium methoxide at a ratio of 0.2–2% as a second catalyst. The reaction was complete in 1–9 h at room temperature. The identity of the amide was confirmed by IR and 13C NMR spectroscopy.
Comparison of steam and nitrogen in the physical deacidification of soybean oil
Authors: Decap Philippe , Braipson‐Danthine Sabine , Vanbrabant Béatrice , De Greyt Wim , Deroanne Claude 
Published: May 2007

AbstractDeacidification in physical refining is one of the most sensitive steps in refining edible vegetable oils because of its large impact on the quality of the oil. The removal of volatile compounds such as FFA is accomplished at elevated temperatures and a high vacuum with a stripping gas, usually steam. The aim of this work was to verify, at the laboratory level, the advantages of using an alternative stripping gas, nitrogen, instead of steam. An ideal vapor‐liquid equilibrium model (IVLE) was used to compare the stripping capacities of steam and nitrogen and to analyze the effects of various operational parameters (temperature, pressure, amount of stripping gas) on the residual acidity of the oil. There was no clear evidence that nitrogen showed a higher capacity to strip FFA than steam. The IVLE model seemed suitable to describe FFA laboratory distillation by using steam or nitrogen, provided the final residual content of FFA was not too low.
Biological network mapping and source signal deduction
Authors: Brynildsen Mark P. , Wu Tung-Yun , Jang Shi-Shang , Liao James C. 
Published: May 2007

AbstractMotivation: Many biological networks, including transcriptional regulation, metabolism, and the absorbance spectra of metabolite mixtures, can be represented in a bipartite fashion. Key to understanding these bipartite networks are the network architecture and governing source signals. Such information is often implicitly imbedded in the data. Here we develop a technique, network component mapping (NCM), to deduce bipartite network connectivity and regulatory signals from data without any need for prior information.Results: We demonstrate the utility of our approach by analyzing UV-vis spectra from mixtures of metabolites and gene expression data from Saccharomyces cerevisiae. From UV-vis spectra, hidden mixing networks and pure component spectra (sources) were deduced to a higher degree of resolution with our method than other current bipartite techniques. Analysis of S.cerevisiae gene expression from two separate environmental conditions (zinc and DTT treatment) yielded transcription networks consistent with ChIP-chip derived network connectivity. Due to the high degree of noise in gene expression data, the transcription network for many genes could not be inferred. However, with relatively clean expression data, our technique was able to deduce hidden transcription networks and instances of combinatorial regulation. These results suggest that NCM can deduce correct network connectivity from relatively accurate data. For noisy data, NCM yields the sparsest network capable of explaining the data. In addition, partial knowledge of the network topology can be incorporated into NCM as constraints.Availability: Algorithm available on request from the authors. Soon to be posted on the web, http://www.seas.ucla.edu/~liaoj/Contact: liaoj@ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online.
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations
Authors: Kerhornou Arnaud , Guigó Roderic 
Published: May 2007

AbstractSummary: Here we present a computational protocol to analyze the promoter regions of a given set of co-expressed genes, and its implementation through the use of Web services technologies. This protocol aims to cluster a set of co-regulated genes in subsets of genes showing similar configurations of transcription factor binding sites. All the steps of this protocol have been developed as web services that are compliant with BioMoby specifications.Availability: {http://genome.imim.es/cgi-bin/moby/GeneClustering_DataSubmission.cgi}Contact: arnaud.kerhornou@crg.esSupplementary information: Supplementary data are available at {http://genome.imim.es/webservices/}
OBO to OWL: a protégé OWL tab to read/save OBO ontologies
Authors: Moreira Dilvan A. , Musen Mark A. 
Published: May 2007

AbstractThe Open Biomedical Ontologies (OBO) format from the GO consortium is a very successful format for biomedical ontologies, including the Gene Ontology. But it lacks formal computational definitions for its constructs and tools, like DL reasoners, to facilitate ontology development/maintenance. We describe the OBO Converter, a Java tool to convert files from OBO format to Web Ontology Language (OWL) (and vice versa) that can also be used as a Protégé Tab plug-in. It uses the OBO to OWL mapping provided by the National Center for Biomedical Ontologies (NCBO) (a joint effort of OBO developers and OWL experts) and offers options to ease the task of saving/reading files in both formats.Availability: bioontology.org/tools/oboinowl/obo_converter.htmlContact: dilvan@stanford.eduSupplementary information: Supplementary data are available at Bioinformatics online.
High-Throughput, High-Sensitivity Analysis of Gene Expression in Arabidopsis
Authors: Kris Richard Martin , Felder Stephen , Deyholos Michael , Lambert Georgina M. , Hinton James , Botros Ihab , Martel Ralph , Seligmann Bruce , Galbraith David W. 
Published: May 2007

AbstractHigh-throughput gene expression analysis of genes expressed during salt stress was performed using a novel multiplexed quantitative nuclease protection assay that involves customized DNA microarrays printed within the individual wells of 96-well plates. The levels of expression of the transcripts from 16 different genes were quantified within crude homogenates prepared from Arabidopsis (Arabidopsis thaliana) plants also grown in a 96-well plate format. Examples are provided of the high degree of reproducibility of quantitative dose-response data and of the sensitivity of detection of changes in gene expression within limiting amounts of tissue. The lack of requirement for RNA purification renders the assay particularly suited for high-throughput gene expression analysis and for the discovery of novel chemical compounds that specifically modulate the expression of endogenous target genes.
Distinct Expression Patterns of Natural Antisense Transcripts in Arabidopsis
Authors: Henz Stefan R. , Cumbie Jason S. , Kasschau Kristin D. , Lohmann Jan U. , Carrington James C. , Weigel Detlef , Schmid Markus 
Published: May 2007

AbstractIt has been shown that overlapping cis-natural antisense transcripts (cis-NATs) can form a regulatory circuit in which small RNAs derived from one transcript regulate stability of the other transcript, which manifests itself as anticorrelated expression. However, little is known about how widespread antagonistic expression of cis-NATs is. We have determined how frequently cis-NAT pairs, which make up 7.4% of annotated transcription units in the Arabidopsis (Arabidopsis thaliana) genome, show anticorrelated expression patterns. Indeed, global expression profiles of pairs of cis-NATs on average have significantly lower pairwise Pearson correlation coefficients than other pairs of neighboring genes whose transcripts do not overlap. However, anticorrelated expression that is greater than expected by chance is found in only a small number of cis-NAT pairs. The degree of anticorrelation does not depend on the length of the overlap or on the distance of the 5′ ends of the transcripts. Consistent with earlier findings, cis-NATs do not exhibit an increased likelihood to give rise to small RNAs, as determined from available small RNA sequences and massively parallel signature sequencing tags. However, the overlapping regions of cis-NATs appeared to be enriched for small RNA loci compared to nonoverlapping regions. Furthermore, expression of cis-NATs was not disproportionately affected in various RNA-silencing mutants. Our results demonstrate that there is a trend toward anticorrelated expression of cis-NAT pairs in Arabidopsis, but currently available data do not produce a strong signature of small RNA-mediated silencing for this process.
UDP-Glucose 4-Epimerase Isoforms UGE2 and UGE4 Cooperate in Providing UDP-Galactose for Cell Wall Biosynthesis and Growth of Arabidopsis thaliana
Authors: Rösti Johannes , Barton Christopher J. , Albrecht Sandra , Dupree Paul , Pauly Markus , Findlay Kim , Roberts Keith , Seifert Georg J. 
Published: May 2007

Abstract
Five Arabidopsis thaliana genes that encode UDP-glucose 4-epimerase (UGE) and represent two ancient plant UGE clades might be involved in the regulation of cell wall carbohydrate biosynthesis. We tested this hypothesis in a genome-wide reverse genetic study. Despite significant contributions of each gene to total UGE activity, none was essential for normal growth on soil. uge2 uge4 displayed dramatic general growth defects, while other mutant combinations were partially aberrant. UGE2 together with UGE3 influenced pollen development. UGE2 and UGE4 synergistically influenced cell wall galactose content, which was correlated with shoot growth. UGE2 strongly and UGE1 and UGE5 lightly supported UGE4 in influencing root growth and cell wall galactose content by affecting galactan content. By contrast, only UGE4 influenced xyloglucan galactosylation in roots. Secondary hypocotyl thickening and arabinogalactan protein carbohydrate structure in xylem parenchyma depended on the combination of UGE2 and UGE4. As opposed to cell wall galactose content, tolerance to external galactose strictly paralleled total UGE activity. We suggest a gradual recruitment of individual UGE isoforms into specific roles. UGE2 and UGE4 influence growth and cell wall carbohydrate biosynthesis throughout the plant, UGE3 is specialized for pollen development, and UGE1 and UGE5 might act in stress situations.