bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dislocated micro‐ and nanopipes with surface steps
Authors: Gutkin M. Yu. , Sheinerman A. G. 
Published: March 2004

AbstractThe steps at the inner surfaces of micro‐ and nanopipes containing screw superdislocations are theoretically investigated and discussed. The stress fields of dislocated pipes with small axially symmetric steps are derived in a closed approximate form. The pipes in an infinite medium as well as the pipes perpendicular to a flat free surface are examined. The forces acting on pipe steps are also calculated, and the equilibrium positions for the steps are found. It is shown that subsurface pipe steps repulse from the free surface if they decrease the pipe radius. It is also demonstrated that the same‐sign steps attract each other (at least, as long as they are small), and so the formation of large enough steps at the pipe surface is possible. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Acoustic wave propagation in layered spherical structures
Authors: Yun‐tuan Fang , Ting‐gen Shen , Xilin Tan 
Published: March 2004

AbstractRadiation from acoustic sources located inside quasi‐periodically layered structures is studied using the transfer matrix method. In contrast to the periodically layered cases the transmission in the quasi‐periodic systems has different band structures and decreases more slowly with the number of layers than in the periodic systems. The transmission periodically changes with the variation of media thickness in both types of systems, which may be useful in designing phonic devices. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Retailers' tagging practices: a potential liability?
Authors: Bix Laura , Sansgiry Sujit S. , Clarke Robert , Cardoso Fernando , Shringarpure Gauri S. 
Published: March 2004

AbstractThis study investigates the coverage of federally mandated information on over‐the‐counter (OTC) drug labels by electronic article surveillance (EAS) tags applied to the exterior of cartons. Using adult‐strength analgesics containing acetaminophen as a case study, researchers investigated the issue in Houston, Texas (24 stores) and Lansing, Michigan (33 stores). The information obscured by EAS tags was identified and classified for a total of 849 packages using a standardized data collection instrument. The results indicated that 293 packages examined, or 34.5%, had information mandated by the US Food and Drug Administration (US FDA) fully or partially obscured by the EAS tags. Retailers and manufacturers should be aware of such practices to reduce potential liability. Recommendations for improving EAS tag usage on OTC products are presented. Copyright © 2004 John Wiley & Sons, Ltd.
High‐pressure processing effects on the mechanical, barrier and mass transfer properties of food packaging flexible structures: a critical review
Authors: Caner Cengiz , Hernandez Ruben J. , Harte Bruce R. 
Published: March 2004

AbstractFood products can be high‐pressure processed (HPP) either in bulk or prepackaged in flexible or semi‐rigid packaging materials. In the latter case the packaging material is subjected, together with the food, to high‐pressure treatment. A number of studies have been performed to quantify the effects of high‐pressure processing on the physical and barrier properties of the packaging material, since the integrity of the package during and after processing is of paramount importance to the safety and quality of the food product. This article reviews the results of published research concerning the effect of HPP on packaging materials. Copyright © 2004 John Wiley & Sons, Ltd.
Oxygen barrier properties of thermoformed trays manufactured with different drawing methods and drawing depths
Authors: Pettersen Marit Kvalvåg , Gällstedt Mikael , Eie Thomas 
Published: March 2004

AbstractA comparison was made of oxygen barrier properties and wall thickness distribution of different thermoformed trays. The thermoformed trays were manufactured with three drawing depths and two different thermoforming methods; with and without plug‐assist. Four different polymer combinations were evaluated. The oxygen transmission rate (OTR) [cm3/(package/day)] was measured at three conditions (23°C/50% relative humidity (RH) with 0% RH inside, 6°C/80% RH with 0% RH inside, and 6°C/80% RH with 100% RH inside. Wall thickness was measured at five different positions in the trays. In general, temperature had more influence on the oxygen transmission rate (OTR) than the humidity. The OTR in the packages increased with increasing drawing depth, but the increase was not linear. Other effects besides thinning, such as orientation, may have influenced the OTR, since the relationship between OTR, given as cm3/(m2/day), and the drawing depth was not linear. Plug‐assisted thermoforming only had an effect on the OTR in trays with 70 mm drawing depth made of 600 µm thick laminate of PP/PE, which was probably due to exceeding the maximum drawing depth of this material. There was no correlation between the OTR value in the packages and the wall thickness in either of the positions, but a quite high correlation between the drawing depth and the relative wall thickness in all measured positions was observed. Copyright © 2004 John Wiley & Sons, Ltd.
Random sampling of 3‐colorings in ℤ2
Authors: Goldberg Leslie Ann , Martin Russell , Paterson Mike 
Published: March 2004

AbstractWe consider the problem of uniformly sampling proper 3‐colorings of an m × n rectangular region of ℤ2. We show that the single‐site “Glauber‐dynamics” Markov chain is rapidly mixing. Our result complements an earlier result of Luby, Randall, and Sinclair, which demonstrates rapid mixing when there is a fixed boundary (whose color cannot be changed). © 2004 Wiley Periodicals, Inc. Random Struct. Alg., 2004
Self‐destructive percolation
Authors: van den Berg J. , Brouwer R. 
Published: March 2004

AbstractConsider ordinary site percolation on an infinite graph in which the sites, independent of each other, are occupied with probability p and vacant with probability 1 − p. Now suppose that, by some “catastrophe,” all sites which are in an infinite occupied cluster become vacant. Finally, each vacant site gets an extra enhancement to become occupied. More precisely, each site that was already vacant or that was made vacant by the catastrophe, becomes occupied with probability δ (independent of the other sites). When p is larger than but close to the critical value pc one might believe (for “nice” graphs) that only a small δ is needed to have an infinite occupied cluster in the final configuration. This appears to be indeed the case for the binary tree. However, on the square lattice we strongly conjecture that this is not true. We discuss the background for these problems and also show that the conjecture, if true, has some remarkable consequences. © 2004 Wiley Periodicals, Inc. Random Struct. Alg., 2004
Exact and approximative algorithms for coloring G(n,p)
Authors: Coja‐Oghlan Amin , Taraz Anusch 
Published: March 2004

AbstractWe investigate the problem of coloring random graphsG(n, p) in polynomial expected time. For the casep≤ 1.01/n, we present an algorithm that finds an optimal coloring in linear expected time. Forp≫ ln6(n)/n, we give algorithms which approximate the chromatic number within a factor ofO( ). We also obtain anO(/ln(np))‐approximation algorithm for the independence number. As an application, we propose an algorithm for deciding satisfiability of random 2k‐SAT formulas overnpropositional variables with ≥ ln7(n)nkclauses in polynomial expected time. © 2004 Wiley Periodicals, Inc. Random Struct. Alg., 2004
Large deviations for sums of partly dependent random variables
Authors: Janson Svante 
Published: March 2004

AbstractWe use and extend a method by Hoeffding to obtain strong large deviation bounds for sums of dependent random variables with suitable dependency structure. The method is based on breaking up the sum into sums of independent variables. Applications are given to U‐statistics, random strings and random graphs. © 2004 Wiley Periodicals, Inc. Random Struct. Alg., 2004
The evolution and population genetics of theALDH2locus: random genetic drift, selection, and low levels of recombination
Authors: Oota Hiroki , Pakstis Andrew J. , Bonne‐Tamir Batsheva , Goldman David , Grigorenko Elena , Kajuna Sylvester L. B. , Karoma Nganyirwa J. , Kungulilo Selemani , Lu Ru‐Band , Odunsi Kunle , Okonofua Friday , Zhukova Olga V. , Kidd Judith R. , Kidd Kenneth K. 
Published: March 2004

SummaryThe catalytic deficiency of human aldehyde dehydrogenase 2 (ALDH2) is caused by a nucleotide substitution (G1510A; Glu487Lys) in exon 12 of theALDH2locus. This SNP, and four non‐coding SNPs, including one in the promoter, span 40 kb ofALDH2; these and one downstream STRP have been tested in 37 worldwide populations. Only four major SNP‐defined haplotypes account for almost all chromosomes in all populations. A fifth haplotype harbours the functional variant and is only found in East Asians. Though the SNPs showed virtually no historic recombination, LD values are quite variable because of varying haplotype frequencies, demonstrating that LD is a statistical abstraction and not a fundamental aspect of the genome, and is not a function solely of recombination. Among populations, different sets of tagging SNPs, sometimes not overlapping, can be required to identify the common haplotypes. Thus, solely because haplotype frequencies vary, there is no common minimum set of tagging SNPs globally applicable. TheFstvalues of the promoter region SNP and the functional SNP were about two S.D. above the mean for a reference distribution of 117 autosomal biallelic markers. These highFstvalues may indicate selection has operated at these or very tightly linked sites.
DNM1DN: a new class of paralogous genomic segments (duplicons) with highly conserved copies on chromosomes Y and 15
Authors: Makrinou E. , Fox M. , Wolfe J. , Cameron J. , Taylor K. , Edwards Y. H. 
Published: March 2004

SummaryScreening a testis cDNA selection library for Y‐linked genes yielded 79 cDNAs. Of these, 9 matched the 3′ region of the dynamin 1 gene (DNM1) on chromosome 9q34 with >90% identity. Fluoresence in situ hybridisation and PCR amplification were used to localise a large number of DNM1‐like sequences to human chromosomes 15 and Y. PCR amplification of overlapping Y‐linked YACs allowed a more accurate mapping of the Y‐linked DNM1‐like cDNAs to a euchromatic locus in close proximity to heterochromatin at Yq11.23. A search of the genome database identified 64 highly homologous copies of the DNM1 fragment. Most of these copies were localised to chromosomes 15 and Y, but others mapped to chromosomes 5, 8, 10, 12, 19 and 22. These sequences exhibit all the major features of a duplicon and have been designated DNM1DN (DNM1 duplicon). Evolutionary studies using fluorescence in situ hybridisation indicate that transposition of the DNM1DN sequence to chromosome 15 took place earlier in primate evolution than the transposition to the Y chromosome. The translocation to the Y took place at a time following the divergence of a common ancestor from gorilla, approximately 4‐7 million years ago.
Population differences in DNA sequence variation and linkage disequilibrium at the PON1 gene
Authors: Koda Y. , Tachida H. , Soejima M. , Takenaka O. , Kimura H. 
Published: March 2004

SummaryPolymorphisms of the promoter region (−108C/T) and the coding region (192Q/R) of the paraoxonase 1 gene (PON1) showed differences in association with cardiovascular disease risk in various populations. To characterize the genetic variation underlying these important polymorphisms, we examined DNA sequence variation both in a 1.3‐kb promoter region 16.5 kb from codon 192, and in a 1.7‐kb region centered on the 192Q/R polymorphic site of the coding region of PON1, in 30 Africans, 30 Europeans and 64 Japanese. We found 10 polymorphic sites and 11 haplotypes in the 1.3‐kb promoter region and 10 biallelic polymorphic sites and 10 haplotypes in the 1.7‐kb region. From the PON1 sequences of chimpanzees and an orangutan, the ancestral type of codon 192 was found to be R. The number of pairs of polymorphic sites between the promoter and 1.7‐kb regions that were in significant linkage disequilibrium was much higher in a Japanese population than in African and European populations. In addition, the pairs of polymorphic sites in linkage disequilibrium differed among the three populations. These results suggest that some of the population differences in association with risk for coronary heart disease can be explained by population differences in haplotype frequency of PON1 haplotypes.
Complex segregation analyses of bone mineral density in Chinese
Authors: Liu P. Y. , Qin Y. J. , Zhou Q. , Recker R. R. , Deng H. W. 
Published: March 2004

SummaryChina has the largest population in the world; approximately 7% of the total population suffers from primary osteoporosis. Osteoporosis is mainly characterized by low bone mineral density (BMD). In the present study, familial correlation and segregation analyses for spine and hip BMDs have been undertaken for the first time in a Chinese sample composed of 401 nuclear families with a total of 1,260 individuals. The results indicate a major gene of additive inheritance for hip BMD, whereas there is no evidence of a major gene influencing spine BMD. Significant familial residual effects are found for both traits, and heritability estimates (±SE) for spine and hip BMDs are 0.807(0.099) and 0.897(0.101), respectively. Sex and age differences in genotype‐specific average BMD are also observed. This study provides the first evidence quantifying the high degree of genetic determination of BMD variation in the Chinese.
Genetic structure and affinities among tribal populations of southern India: a study of 24 autosomal DNA markers
Authors: Vishwanathan H. , Deepa E. , Cordaux R. , Stoneking M. , Usha Rani M. V. , Majumder P. P. 
Published: March 2004

SummaryWe describe the genetic structure and affinities of five Dravidian‐speaking tribal populations inhabiting the Nilgiri hills of Tamil Nadu, in south India, using 24 autosomal DNA markers. Our goals were: (i) to examine what evolutionary forces have most significantly impacted south Indian tribal genetic variation, and (ii) to test whether the phenotypic similarities of some south Indian tribal groups to Africans represent a signature of close relationship to Africans or are due to convergence. All loci were polymorphic and average heterozygosities were substantial (range: 0.347–0.423). Genetic differentiation was high (Gst= 6.7%) and genetic distances were not significantly correlated with geographic distances. Genetic drift therefore probably played a significant role in shaping the patterns of genetic variation observed in southern Indian tribal populations. Otherwise, analyses of population relationships showed that Indian populations are closely related to one another, regardless of phenotypic characteristics, and do not show particular affinities to Africans. We conclude that the phenotypic similarities of some Indian groups to Africans do not reflect a close relationship between these groups, but are better explained by convergence.
A new algorithm for haplotype‐based association analysis: the Stochastic‐EM algorithm
Authors: Tregouet D. A. , Escolano S. , Tiret L. , Mallet A. , Golmard J. L. 
Published: March 2004

SummaryIt is now widely accepted that haplotypic information can be of great interest for investigating the role of a candidate gene in the etiology of complex diseases. In the absence of family data, haplotypes cannot be deduced from genotypes, except for individuals who are homozygous at all loci or heterozygous at only one site. Statistical methodologies are therefore required for inferring haplotypes from genotypic data and testing their association with a phenotype of interest. Two maximum likelihood algorithms are often used in the context of haplotype‐based association studies, the Newton‐Raphson (NR) and the Expectation‐Maximisation (EM) algorithms. In order to circumvent the limitations of both algorithms, including convergence to local minima and saddle points, we here described how a stochastic version of the EM algorithm, referred to as SEM, could be used for testing haplotype‐phenotype association. Statistical properties of the SEM algorithm were investigated through a simulation study for a large range of practical situations, including small/large samples and rare/frequent haplotypes, and results were compared to those obtained by use of the standard NR algorithm. Our simulation study indicated that the SEM algorithm provides results similar to those of the NR algorithm, making the SEM algorithm of great interest for haplotype‐based association analysis, especially when the number of polymorphisms is quite large.
A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I
Authors: Zhang Ren , Zhang Chun-Ting 
Published: March 2004

Abstract
Motivation: Some genomic islands contain horizontally transferred genes, which play critical roles in altering the genotypes and phenotypes of organisms, and horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. A windowless method to display the distribution of genomic GC content, the cumulative GC profile, is proposed to identify genomic islands in genomes whose complete genome sequences are available. Two new indices are proposed to assess the codon usage bias and amino acid usage bias in genomic islands.
Results: A 211 kb genomic island (CGGI-1) has been identified in the genome of Corynebacterium glutamicum, and three genomic islands VVGI-1, VVGI-2 and VVGI-3, with lengths 167, 40 and 33 kb, respectively, have been identified in the genome of Vibrio vulnificus CMCP6 chromosome I. The CGGI-1 is flanked by two ∼500 bp direct repeats, and utilizes a Val-tRNA as the integration site. For the VVGI-1 and VVGI-2, each has an integrase gene at 5′ junction. All the identified genomic islands show unusual GC content, codon usage and amino acid usage, compared with the rest of the genomes. In addition, it is found that genomic islands are fairly homogenous in terms of GC content variation. An index, h, to quantify the homogeneity of GC content for genomic islands is proposed, and it is shown that h is less than 0.1 for all the genomic islands analyzed. The cumulative GC profile, as well as various indices to assess the codon usage bias, amino acid usage bias and homogeneity of the genomic islands, will be useful in the analysis of other genomes.
Availability: Programs used in this work and numerical results are available upon request.
Enhancing scatterplots with smoothed densities
Authors: Eilers Paul H. C. , Goeman Jelle J. 
Published: March 2004

Abstract
Motivation: Scatterplots of microarray data generally contain a very large number of dots, making it difficult to get a good impression of their distribution in dense areas.
Results: We present a fast and simple algorithm for two-dimensional histogram smoothing, to visually enhance scatterplots.
Availability: Functions for Matlab and R are available from the corresponding author.
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments
Authors: Shah Nameeta , Couronne Olivier , Pennacchio Len A. , Brudno Michael , Batzoglou Serafim , Bethel E. Wes , Rubin Edward M. , Hamann Bernd , Dubchak Inna 
Published: March 2004

Abstract
Motivation: The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships.
Results: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments.
Availability: Phylo-VISTA is available at http://www-gsd.lbl.gov/phylovista. It requires an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu
Optimization models for cancer classification: extracting gene interaction information from microarray expression data
Authors: Antonov Alexey V. , Tetko Igor V. , Mader Michael T. , Budczies Jan , Mewes Hans W. 
Published: March 2004

Abstract
Motivation: Microarray data appear particularly useful to investigate mechanisms in cancer biology and represent one of the most powerful tools to uncover the genetic mechanisms causing loss of cell cycle control. Recently, several different methods to employ microarray data as a diagnostic tool in cancer classification have been proposed. These procedures take changes in the expression of particular genes into account but do not consider disruptions in certain gene interactions caused by the tumor. It is probable that some genes participating in tumor development do not change their expression level dramatically. Thus, they cannot be detected by simple classification approaches used previously. For these reasons, a classification procedure exploiting information related to changes in gene interactions is needed.
Results: We propose a MAximal MArgin Linear Programming (MAMA) method for the classification of tumor samples based on microarray data. This procedure detects groups of genes and constructs models (features) that strongly correlate with particular tumor types. The detected features include genes whose functional relations are changed for particular cancer types. The proposed method was tested on two publicly available datasets and demonstrated a prediction ability superior to previously employed classification schemes.
Availability: The MAMA system was developed using the linear programming system LINDO http://www.lindo.com. A Perl script that specifies the optimization problem for this software is available upon request from the authors.