bluuebunny/crossref_metadata_2025 huggingface dataset:
Population Differentiation: Measures
Authors: Mona Stefano , Bertorelle Giorgio
Published: October 2009

The genetic divergence between populations can be quantified using different measures. The crucial parameters of the population structure, divergence times and migration rates, can be estimated using polymorphism data.
Stationary Allele Frequency Distributions
Authors: Rannala Bruce
Published: October 2009

Forces that determine the allele frequencies in natural populations include genetic drift, natural selection, migration and mutation. A balance of opposing forces can, in some cases, cause allele frequencies to approach a stationary distribution over time. The form of this distribution is not influenced by initial allele frequencies, but instead is determined by the relative magnitudes of different evolutionary forces.
Stored Genetic Material: Use in Research in the United Kingdom
Authors: Skene Loane
Published: October 2009

The use of stored genetic material depends on how it was obtained and the consent that was given by the original person. If that person was fully informed and consented to the material being used in research, it is lawful to use it in research following guidelines for ethical conduct. If consent was not or cannot be obtained, the tissue may be used in research but the research should be done only on anonymized and unlinked samples, subject to ethical approval.
Microarray Bioinformatics
Authors: Stubbs Andrew P , Van Yper Stefan JL , van der Spek Peter J
Published: October 2009

Bioinformatics covers the application of computational tools for expanding the use of biological, medical or health‐related data. This includes tools to handle, acquire, store, organize, archive, analyse or visualize data.
Divergence between the Human and Chimpanzee Genomes and its Impact on Protein and Transcriptome Evolution
Authors: Kehrer‐Sawatzki Hildegard , Cooper David N
Published: October 2009

Comparison of the human and chimpanzee genome has revealed a broad spectrum of genetic differences. Although the nucleotide sequence divergence is low (approximately 1%) within those regions that can be aligned, lineage‐specific submicroscopic inversions, insertions and deletions have markedly increased the genetic divergence. The lineage‐specific expansion of gene families, instances of gene inactivation and loss, the accelerated evolution of genes and changes in gene expression may all have been involved in the evolutionary emergence of human‐specific traits. However, it is difficult to distinguish the neutral from the functionally meaningful changes that have occurred in both primate genomes since divergence from their common ancestor.
Evolutionarily Conserved Noncoding DNA
Authors: Jegga Anil G , Aronow Bruce J
Published: October 2009

The availability of increasingly complete and accurate genomic sequence data from evolutionarily separated species – as well as diverse strains and ethnic variants within species – is providing an unprecedented opportunity to identify potentially functional regions within genomic noncoding
deoxyribonucleic acid
(DNA). A variety of bioinformatics tools enable genome‐wide detection, characterization and visualization of highly conserved sequences and the occurrence of potentially functional elements within both the conserved and evolved elements.
ATP‐binding Cassette (ABC) Transporter Supergene Family: Genetics and Evolution
Authors: Dean Michael
Published: October 2009

The adenosine triphosphate (ATP)‐binding cassette (ABC) genes encode transporters that are expressed on the cell membrane or organelle membranes and are involved in the export of substances out of the cell or the movement of compounds inside the cell. Many ABC genes are mutated in human diseases or have a role in drug resistance to cancer chemotherapy.
Pathological Missense Mutations Provide New Insights into the Evolution of Trypsinogen Genes
Authors: Chen Jian‐Min , Cooper David N , Férec Claude
Published: October 2009

Mutations in pathology and evolution represent two sides of the same coin in that disease‐causing mutations tend to be found at those amino acid positions that exhibit the highest degree of evolutionary conservation. An archetypal example of the inter‐relationship between pathology and evolution is provided by trypsinogen. Thus, studies of disease‐causing mutations in the human cationic
trypsinogen
gene (

PRSS1

) have revealed evidence for past gene conversion events between the various gene family members. A combination of the functional characterization of subtle missense mutations with comparative sequence analysis has also revealed evidence for the action of natural selection operating on the
trypsinogens
during mammalian/vertebrate evolution.
Morphological Diversity: Evolution
Authors: Budd Graham
Published: October 2009

Morphology has diversified through the evolutionary process. However, its structure and relationship to the genome are both complex, making its evolution hard to understand.
Visual Pigment Genes: Evolution
Authors: Yokoyama Shozo
Published: October 2009

More than 100 visual pigment genes have been cloned from a diverse range of vertebrates. Comparative sequence analyses of these genes and

in vitro

assays of engineered visual pigments have been used to elucidate not only the molecular bases of color vision but also the processes of adaptive evolution at the molecular level.
Segmental Duplications and Genetic Disease
Authors: Emanuel Beverly S , Shaikh Tamim H
Published: October 2009

More than 50% of our genome is made up of repetitive DNA elements, which are classified into different categories based on their size, copy number, mechanisms of dispersal and several other factors. Segmental duplications represent one such class of repetitive element. Recently, several genetic diseases have been shown to be the result of chromosomal rearrangements mediated by segmental duplications.
Peopling of India: Insights from Genetics
Authors: Majumder Partha P
Published: October 2009

Genes move as people move. Therefore, it is possible to reconstruct trails of human migration by studying genetic characteristics of people from different regions of the world. Humankind evolved out of Africa and moved out of Africa to populate different parts of the world. One of the earliest waves of human migration from out‐of‐Africa came into India. Genetic data have been helpful in reconstructing the processes of peopling of India and the relationships among contemporary ethnic groups of India. This article provides an overview of these findings.
Roma (Gypsies): Genetic Studies
Authors: Morar Bharti , Kalaydjieva Luba
Published: October 2009

The Roma, also known as Gypsies, are a transnational founder population, resembling a mosaic of socially and genetically divergent groups. Common origins from a small group of related founders result in sharing of maternal and paternal lineages and of ancient disease‐causing mutations across endogamous Romani groups in different countries. Genetic differentiation between groups, with an impact on genetic epidemiology, is the product of bottleneck events, random genetic drift and differential admixture, and correlates with the migrational history of the Roma in Europe.
Restoration and Creation of Freshwater and Estuarine Wetlands
Authors: Fennessy M Siobhan , Herbert Ellen R
Published: October 2009

The restoration and creation of freshwater and estuarine wetlands are important practices designed to increase wetland acreage and mitigate for the extensive losses of wetland area all over the world. Wetland restoration, defined as the reestablishment of wetlands where they once existed, and wetland creation, where entirely new wetlands are established in upland locations, require an understanding of hydrology, soils and landscape setting to foster the development of native biotic communities, including vegetation, invertebrates and amphibians. Restoration projects may take decades to fully develop; success may be measured by comparison of key indicators with natural wetlands.
Climate Change Impacts: Birds
Authors: Gienapp Phillip
Published: October 2009

Climate change can affect populations and species in various ways, many of which are well documented in birds. For example, the geographical distribution of species has shifted poleward and to higher altitudes, birds are nowadays breeding or migrating earlier. Ultimately interesting is how these changes affect population processes and thereby possibly persistence. So far, it is however unclear how strong the impact of climate change will and what role adaptation can play to mitigate its effects.
Plant Virus Movement
Authors: Taliansky Michael E , Torrance Lesley
Published: October 2009

Plant virus movement is the process of the spread of virus genetic material from the initially infected cells to the rest of the plant. There are several distinct stages including intracellular movement from sites of virus replication out of the initially infected cell, cell‐to‐cell trafficking through plasmodesmata (plant‐specific intercellular membranous channels) and long‐distance movement between organs through the phloem (the specialized vascular system used by plants for the transport of assimilates and macromolecules).
Y
Chromosome Evolution
Authors: Gvozdev Vladimir A
Published: October 2009

The evolution of the Y chromosomes of different taxa (humans, plants and
Drosophila
) is considered as well as the degeneration processes that affected the autosomal ancestor (proto‐Y chromosome). The acquisition of testis‐expressed genes and their amplifications on the Y chromosome are discussed. In spite of the differences and the specificity of evolutionary forces driving their diversification, the molecular studies of the Y chromosomal structures reveal some unexpected similarities in different evolutionary lineages.
The Chimpanzee Genome Project
Authors: Cooper David N , Kehrer‐Sawatzki Hildegard
Published: October 2009

In 2005, a draft genome sequence of the common chimpanzee (

Pan troglodytes

) was published by the Chimpanzee Sequencing & Analysis Consortium (CSAC). This sequence has allowed us to catalogue the genetic differences which have accumulated since humans and chimpanzees diverged from their common ancestor 5–7 million years ago. These differences include approximately 35 million single‐nucleotide substitutions and 5 million insertion/deletion events within the alignable regions. This catalogue of differences has been used to assess the magnitude and regional variation of the mutational forces which have shaped the two genomes, and to measure the strength of positive and negative selection acting on their genes.
Selective Constraints and Human Disease Genes: Evolutionary and Bioinformatics Approaches
Authors: Dopazo Hernán
Published: October 2009

Natural selection rejects with variable strength, mutations reducing the individual's capability to survive and reproduce. Evolutionary theory predicts that mutations producing disease will be under strong selective constraints. Selective strength at the codon level will determine if mutation frequency will increase, decrease or change randomly during evolution. This strength finally serves in the prediction of nonsynonymous single nucleotide polymorphisms (nsSNPs) producing disease in humans. By using comparative genomics data and maximum likelihood phylogenetics approaches we demonstrate that mutations on residues showing low rates of evolution are significantly associated to disease and not to human genetic polymorphisms.
Human and Chimpanzee Transcriptomes: Comparative Evolution
Authors: Khaitovich Philipp , Kehrer‐Sawatzki Hildegard , Cooper David N
Published: October 2009

The biological basis of the uniqueness of human abilities is one of the most fascinating research topics of all time. Evolutionary studies now allow us, at least in principle, to identify the underlying functional genetic elements which are specific to humans. However, despite enormous progress in the biosciences over recent years, which has resulted in the complete sequencing of the human genome as well as the genomes of two closely related primate species – chimpanzee and rhesus macaque – the molecular mechanisms underlying human‐specific abilities remain unknown. Gene expression studies now provide us with a powerful tool to identify the functional differences distinguishing humans from chimpanzees, our closest living relatives. From the evolutionary and functional perspective, however, the interpretation of the observed expression differences is almost never as straightforward as we would ideally like.
Human Transcriptome Evolution
Authors: Gu Xun , Huang Yong
Published: October 2009

It has been a long‐standing hypothesis that evolution of the human transcriptome (the collection of all gene transcripts in a cell) may have contributed greatly to the observed human‐specific phenotypes. With recent advances in high throughput technologies and bioinformatic tools, it becomes possible to get deep understandings of this important issue. Here, we provided a brief but updated summary of the exciting findings in the study of human transcriptome evolution.
Evolutionary Emergence of Genes Through Retrotransposition
Authors: Cordaux Richard , Batzer Mark A
Published: October 2009

Variation in the number of genes among species indicates that new genes are continuously generated over evolutionary times. Evidence is accumulating that transposable elements, including retrotransposons (which account for about 90% of all transposable elements inserted in primate genomes), are potent mediators of new gene origination. Retrotransposons have fostered genetic innovation during human and primate evolution through: (i) alteration of structure and/or expression of pre‐existing genes following their insertion, (ii) recruitment (or domestication) of their coding sequence by the host genome and (iii) their ability to mediate gene duplication via ectopic recombination, sequence transduction and gene retrotransposition.
Olfactory Receptor Genes: Evolution
Authors: Niimura Yoshihito
Published: October 2009

There are ∼1000 olfactory receptor genes in mammals, forming the largest multigene family. Identification of the entire repertoires of olfactory receptor genes from various species and extensive phylogenetic analyses revealed dynamic change of this gene family in evolution.
Rapidly Evolving Regions of the Human Genome
Authors: Agarwal Subhash Mohan
Published: October 2009

Rapidly evolving genes
are those genes that exhibit accelerated rates of nonsynonymous substitutions between species, i.e. the number of nonsynonymous substitutions per nonsynonymous site (amino acid altering) significantly exceeds the number of synonymous substitutions per synonymous site.
Genetics and the Origins of the Chinese
Authors: Kong Qing‐Peng , Pan Hui , Zhang Ya‐Ping
Published: October 2009

China is an extremely important region in anthropology not only for its enormous population size and diversely morphological, cultural and linguistic characteristics, but also for its abundant and successive hominid fossil records. Tracing the origin of modern Chinese and reconstructing its prehistory undoubtedly become one of the most intriguing and challenging issues for scientists.
Endogenous Retroviral Sequences; their Evolutionary Contribution to the Human Genome
Authors: Mayer Jens
Published: October 2009

Endogenous retroviruses
(ERVs) comprise about 8% of the human genome. They stem from germ cell invasions of exogenous
retroviruses
in the evolutionary past. ERV transcripts are found in every human tissue and their expression patterns seem to be regulated by complex mechanisms. By introducing numerous regulatory elements into the genome ERVs profoundly influenced cellular genes regarding gene structure and gene expression patterns. While most ERV sequences in the human genome are coding‐defective, some ERVs still encode proteins that appear to have become essential human genes or that appear to be involved in human diseases.
Human Endogenous Retroviruses; Evolutionary Dynamics, Chromosomal Location and Host Benefit
Authors: Nelson Paul , Freimanis Graham , Roden Denise
Published: October 2009

Human endogenous retroviruses (HERVs) are remnants of past retroviral infection that have been integrated within the human genome. Our glimpse of these viruses perhaps highlights their evolutionary dynamics over time. Survival of both virus and host are paramount and it is plausible that some benefit has arisen whereby the human host has gained some selective advantage. In particular, some retroviral elements may have regulatory or biological functions. Of course harbouring viruses could also lead to harm if activated by environmental agents.
The Impact of Gene Duplication on Human Genome Evolution
Authors: Cotton James A
Published: October 2009

Gene duplication has had a significant impact on all genomes and the human genome is no exception, as gene duplication contributes much of the raw material from which natural selection shapes novel genes. In the context of human evolution, interest in gene duplication has been intense as the human genome is particularly rich in duplicated genomic regions. These duplicate genes contribute to genomic instability, leading to genome rearrangement and speciation. Recent evidence suggests that duplicated genes have undergone greater diversification than other loci in the human lineage, and so have been key in the evolution of uniquely human traits.
Evolution of X‐chromosome Inactivation
Authors: Shevchenko Alexander I , Zakian Suren M
Published: October 2009

X‐chromosome inactivation is a transcriptional silencing of one of the two X chromosomes that occurs in females of marsupial and eutherian mammals. The process arose and developed as a mechanism of dosage compensation during differentiation of mammalian X and Y chromosomes. X inactivation started from being imprinted and unstable in marsupials and then was transformed to random and stabile in eutherians.
Positive Selection on Genes in Humans as Compared to Chimpanzees
Authors: Bakewell Margaret A , Zhang Jianzhi
Published: October 2009

Positive selection has been identified and extensively studied in many human genes. In contrast, positive selection in the closest human relative, chimpanzee, has been largely unstudied until recently. With the complete sequencing of the human and chimpanzee genomes, a comparison of the types and numbers of genes that underwent positive selection in the two species is possible. The types of genes under positive selection in human and chimpanzee are different with regard to gene function, but no particular type accounts for a large part of this difference. However, significantly more genes experienced positive selection in the chimpanzee lineage than in the human lineage.
Recombination and Human Genetic Diversity
Authors: Spencer Chris CA
Published: October 2009

With the advent of genome‐wide human genetic data, understanding the role of recombination in determining patterns of genetic diversity is more important than ever before. Hotspots of recombination are now known to be a key component in dictating the structure of diversity in human populations, and recent research suggests they may play a more fundamental role in the evolution of the human genome.
Rapid Evolution of Genes on the Human X‐chromosome
Authors: Kvikstad Erika M , Makova Kateryna D
Published: October 2009

Owing to sex chromosome‐specific modes of natural selection, genes on the human X‐chromosome are evolving rapidly in comparison to genes located on autosomes. Biological factors additional to selection could contribute to these elevated rates, including evolutionary history and genomic features of the X‐chromosome. Furthermore, genes on the X are distributed in a nonrandom fashion, potentially influencing their evolution. Finally, the function and expression of each X‐linked gene may play a role in determining its evolutionary rate.
The Neo‐selectionist Theory of Genome Evolution
Authors: Bernardi Giorgio
Published: October 2009

The role of chance in evolution is a central problem in biology, as illustrated, for instance, by Monod's book
Chance and Necessity
(1971). The present article will first sketch the classical evolutionary theories proposed since Darwin and the approaches used to study evolution, then focus on the recently proposed neo‐selectionist theory (Bernardi, 2007). At variance with the classical theories, the neo‐selectionist theory had its basis on observations made on the organization and the evolution of the eukaryotic genome, in particular of the vertebrate genome. This approach was started many years ago, but could recently take advantage of the availability of full genome sequences. Interestingly, the neo‐selectionist theory not only provides a solution to the neutralist/selectionist debate, but also introduces an epigenomic component in genome evolution.
Biomolecular
NMR
Spectroscopy of Ribonucleic Acids
Authors: Dieckmann Thorsten , Legault Pascale
Published: October 2009

Biomolecular nuclear magnetic resonance (NMR) spectroscopy allows the characterization of structural and dynamic properties of ribonucleic acids (RNAs) in solution. The NMR‐based determination of high‐resolution three‐dimensional (3D) structures has been achieved for RNAs up to
ca
. 100 nucleotides. Biomolecular NMR also provides valuable information about RNA–ligand interactions and the role of metal ions and shifted p
K
a
in RNA structure and catalysis.
Ptitsyn, Oleg
Authors: Finkelstein AV , Bychkova VE
Published: October 2009

The Russian biophysicist and polymer physicist (1929–1999) who discovered the ‘molten globule’ state of proteins and developed the first statistic theory of macromolecules.
Farmer exposure to organic solvents during the maintenance and repair of farm machinery: A pilot study
Authors: Bunn Terry L. , Liu Youcheng , Lee Kiyoung , Robertson Medearis , Yu Lei
Published: October 2009

Background

The maintenance/repair of farm machinery is a common farming activity. Dermal exposure to organic solvents has not been well documented. A pilot study was conducted to characterize exposure to organic solvents.

Methods

A survey questionnaire was administered to 31 Kentucky farmers in 2008. Dermal exposure assessment was conducted in 10 farmers while farmers performed farm machinery maintenance/repair tasks using a solvent sampling patch. Benzene, toluene, xylene, and n‐hexane were analyzed.

Results

All four organic solvents were identified from the samples with toluene (<0.5–36,000 µg/patch) and xylene (15–5,700 µg/patch) at significantly higher levels. Twenty‐six farmers reported the use of personal protective equipment <50% of their time repairing/maintaining farm machinery on the questionnaire; only two farmers wore gloves during the exposure assessment.

Conclusions

Farmers routinely use solvent products for farm machinery maintenance/repair. Dermal exposure to organic solvents is a potential hazard. Further studies to characterize and evaluate exposure in larger samples of farmers are needed. Am. J. Ind. Med. 52:973–981, 2009. © 2009 Wiley‐Liss, Inc.
Improved dewatering by freeze–thawing of predewatered sludge cakes
Authors: Saveyn H. , Curvers D. , Jacobsen R. , Van der Meeren P.
Published: November 2009

Biological sludge dewatering is known to be a troublesome operation due to the nature of the raw material. Dry matter contents of more than 30% are seldom obtained, leaving a final product containing more than two thirds of water. Many approaches have been used to improve the dewatering step by influencing the conditioning or dewatering process. One of the physical conditioning methods used is freeze–thawing, in which the physical structure of the sludge is destroyed. Most studies so far have been focusing on freeze–thawing of sludge at low solids concentrations, making it an inefficient process with regard to energy and cost. This study focuses on the freeze–thawing of predewatered sludges for subsequent mechanical dewatering in order to reduce the final sludge volume and hence disposal costs. Predewatered sludge with a dry matter content of 25–30% was frozen for different times periods (1–96 h) and at different temperature gradients (slow to fast freezing) using a variety techniques (submersion in glycol, commercial freezer and liquid nitrogen). The results from this study indicated that thawing followed by a second mechanical dewatering resulted in dry matter contents of up to 50%. Slow freezing times and long storage times yielded the best dewaterability results. An economical assessment of the process showed that a depreciation time of 2 years already delivers a profitable process. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd.
Plasma‐induced, solid‐state polymerization of N‐isopropylacrylamide
Authors: Unver Alper , Akovali Guneri
Published: November 2009

The radio‐frequency plasma‐initiated polymerization of N‐isopropylacrylamide (NIPAM) in the solid state was performed. The isolated linear polymer was characterized by 13C‐NMR, 1H‐NMR, and Fourier transform infrared spectroscopy, and the effects of selected operational plasma parameters (discharge power and time) on the conversion rates were studied. Reversible transitions at the volume‐phase‐transition temperatures of the swelled poly(N‐isopropylacrylamide) hydrogels were investigated by differential scanning calorimetry. The surface morphologies before and after plasma treatment were followed by scanning electron microscopy. With the obtained X‐ray diffraction results, we propose a solid‐state plasma polymerization mechanism for the NIPAM. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Multifunctional anionic cotton dyeings
Authors: Ibrhim N. A. , Mahrous F. , El‐Gamal A. R. , Gouda M. , Husseiny S. M.
Published: November 2009

Anionic cotton dyeings with anti‐ultraviolet and antibacterial functions were prepared by the post‐treatment of direct and reactive cotton dyeings with a zirconium oxychloride salt solution. The extent of improvement in the functional properties was governed by the structure and pretreatment history of the knitted cotton fabric, the kind and concentration of the anionic dye, and the dyeing regime. The chelation and fixation of the positively charged zirconium ions onto and/or within the dyed substrate resulted in an enhancement in the ultraviolet absorption capacity of the treated substrate and interaction with the thiol groups of the cellular protein; this imparted antibacterial activity against Gram‐positive and Gram‐negative bacteria without adverse effects on the hue of the obtained dyeings. Both the anti‐ultraviolet and bacterial functions of the post‐treated dyeings survived through 15 washing cycles. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Thermomechanical characterization of thermoset urethane shape‐memory polymer foams
Authors: Domeier Linda , Nissen April , Goods Steven , Whinnery LeRoy , McElhanon James
Published: November 2009

The shape‐memory polymer performance of urethane foams compressed under a variety of conditions was characterized. The foams were water‐blown thermosets with a closed‐cell structure and ranged in density from about 0.25 to 0.75 g/cm3. Compressive deformations were carried out over a range of strain levels, temperatures, and lateral constraints. Recovery stresses measured between fixed platens were as high as 4 MPa. Recovery strains, measured against loads up to 0.13 MPa, demonstrated the effects of various parameters. The results suggest that compression near the foam glass‐transition temperature provided optimal performance. Foams with densities of about 0.5 g/cc and compressed 50% provided a useful balance (time, strain, and load) in the recovery performance. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Social validation of collective annotations: Definition and experiment
Authors: Cabanac Guillaume , Chevalier Max , Chrisment Claude , Julien Christine
Published: November 2009

People taking part in argumentative debates through collective annotations face a highly cognitive task when trying to estimate the group's global opinion. In order to reduce this effort, we propose in this paper to model such debates prior to evaluating their “social validation.” Computing the degree of global confirmation (or refutation) enables the identification of consensual (or controversial) debates. Readers as well as prominent information systems may thus benefit from this information. The accuracy of the social validation measure was tested through an online study conducted with 121 participants. We compared their human perception of consensus in argumentative debates with the results of the three proposed social validation algorithms. Their efficiency in synthesizing opinions was demonstrated by the fact that they achieved an accuracy of up to 84%.
State waypoint approach to continuous‐time nonlinear optimal control problems
Authors: Honarvarmahjoobin Mohamadhadi , Tazaki Yuichi , Imura Jun‐ichi
Published: November 2009

In this paper, we propose an optimal control technique for a class of continuous‐time nonlinear systems. The key idea of the proposed approach is to parametrize continuous state trajectories by sequences of a finite number of intermediate target states; namely, waypoint sequences. It is shown that the optimal control problem for transferring the state from one waypoint to the next is given an explicit‐form suboptimal solution, by means of linear approximation. Thus the original continuous‐time nonlinear control problem reduces to a finite‐dimensional optimization problem of waypoint sequences. Any efficient numerical optimization method, such as the interior‐reflection Newton method, can be applied to solve this optimization problem. Finally, we solve the optimal control problem for a simple nonlinear system example to illustrate the effectiveness of this approach. Copyright © 2009 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
Stability analysis for discrete‐time fuzzy system by utilizing homogeneous polynomial matrix function
Authors: Wang Likui , Liu Xiaodong
Published: November 2009

The purpose of this paper is to investigate the stability of nonlinear systems represented by a Takagi‐Sugeno discrete‐time fuzzy model. The homogeneous polynomial matrix function (HPMF) is developed to obtain new stabilization conditions. Applying the HPMF to the non‐parallel distributed compensation (non‐PDC) law and non‐quadratic Lyapunov function, some new stabilization conditions are obtained by the following two means: (a) utilizing the popular idea of introducing additional variables for some fixed degree of the HPMF; and (b) increasing the degree of the HPMF. It is shown that the conditions obtained with approach (a) are less conservative than some sufficient stability conditions available in the literature to date. It is also shown that as the degree of HPMF increases the conditions obtained under (b) become less conservative. An example is provided to illustrate how the proposed approaches compare with other techniques available in the literature. Copyright © 2009 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
In search of antioxidants and anti‐atherosclerotic agents from herbal medicines
Authors: Shiao Ming‐Shi , Chiu Jing‐Jing , Jen Wei‐Ping , Chang Bao‐Wen , Wang Jane , Wu Ye‐Jer , Chen Yuh‐Lien
Published: November 2009

Many recent studies have suggested that low‐density lipoprotein (LDL) oxidation, endothelial dysfunction, and inflammation are involved in the pathogenesis of atherosclerosis. Herbal regimens in the treatment of blood stasis, a counterpart of atherosclerosis, commonly use medicinal plants of leguminosae and labiatae. We have developed disease‐oriented screening methods to search for bioactive components, particularly isoflavones in leguminosae and polyphenols in labiatae from Chinese herbal medicines. Many bioactive components and active fractions capable of inhibiting a. Cu(II)‐induced LDL oxidation, b. oxidized LDL‐induced endothelial damage, c. uptake of oxidized LDL by macrophages (J774A.1), and d. expression of cell adhesion molecules (CAMs) have been identified. A polyphenol, namely salvianolic acid B from Salvia miltiorrhiza was identified to be a potent antioxidant, endothelial‐protecting agent, and an inhibitor to suppress the expression of ICAM and VCAM. This review also briefly describes the strategy for developing herbal medicines as anti‐atherosclerotic agents.
Lipid peroxidation products as oxidative stress biomarkers
Authors: Niki Etsuo
Published: November 2009

Oxidative stress induced by reactive oxygen and nitrogen species has been implicated in the pathogenesis of various disorders and diseases. Biomarkers are needed for assessment of oxidative stress status in vivo and also for health examination, diagnosis at early stage, prognosis, safe and efficient drug development, and evaluation of efficacy of drugs, foods, beverages, and supplements. Lipids are susceptible to oxidation and lipid peroxidation products are potential biomarkers for oxidative stress status in vivo and its related diseases. Recently, isoprostane, isoprostaglandin homologues from arachidonic acid, neuroprostanes from docosahexaenoic acid, hydroxyoctadecadienoic acid from linoleic acid, and oxysterols from cholesterol have received much attention as potential biomarkers for oxidative stress status in vivo. The physiological levels of these lipid peroxidation products and potential application as biomarkers will be reviewed.
Transplasma membrane electron transport comes in two flavors
Authors: Lane Darius J. R. , Lawen Alfons
Published: November 2009

All tested cells possess transplasma membrane electron transfer (tPMET) systems that are capable of reducing extracellular electron acceptors at the cost of cytosolic electron donors. In mammals, classically NAD(P)H‐ and NADH‐dependent systems have been distinguished. The NADH‐dependent system has been suggested to be involved in non‐transferrin‐bound iron (NTBI) reduction and uptake. Recently we reported that transplasma membrane ascorbate/dehydroascorbate cycling can promote NTBI reduction and uptake by human erythroleukemia (K562) cells (D.J.R. Lane and A. Lawen,J Biol Chem283 (2008), 12701‐12708). This system, involves i) cellular import of dehydroascorbate, ii) intracellular reduction of dehydroascorbate to ascorbate using metabolically‐derived reducing equivalents, iii) export of ascorbate down its concentration gradient, iv) direct reduction of low molecular weight iron chelates by ascorbate, and v) uptake of iron (II) into the cell. We here propose the consideration of this system as a novel form of tPMET which shares with classical enzyme‐mediated tPMET systems the net transfer of reducing equivalents from the cytoplasmic compartment to the extracellular space, but lacks the involvement of the plasma membrane oxidoreductases responsible for the latter. Thus, transplasma membrane electron transfer can and does occur at two mechanistically distinct levels: i) enzyme‐mediated transmembrane electron transfer and ii) transmembrane metabolite shuttling/cycling.
Effect of Ccapsaicin on tNOX (ENOX2) protein expression in stomach cancer cells
Authors: Wang Hsi‐Ming , Chueh Pin Ju , Chang Sheng‐Pang , Yang Chi‐Lien , Shao Kuo‐Ning
Published: November 2009

Tumor‐associated NADHoxidase (tNOX, also known as ENOX2) is a growth‐related protein expressed in transformed cells. Previous reports have revealed that the inhibition of tNOX activity by the anti‐cancer drug, capsaicin, correlates with a reduction in growth of cancer cells, indicating a close relationship between tNOX activity and cell growth. Moreover, the study of depleted tNOX expression by RNA interference in HeLa cells suggests that it may be associated with the ability of tumor cells to acquire an aggressive phenotype, particularly in relation to cell proliferation. A key role for tNOX in regulating cell growth is further supported by the observation that the growth rate of MEF cells from tNOX‐overexpressing transgenic mice is approximately two‐fold greater than that of wild‐type cells. The purpose of this study was to investigate the anti‐proliferative effect of capsaicin on tNOX expression level in stomach cancer cells. We showed that capsaicin induced cytotoxicity in SCM cells concomitantly with apoptosis, PARP cleavage, and down‐regulation of tNOX protein.
Cancer cells with high expression of CD133 exert FLIP upregulation and resistance to TRAIL‐induced apoptosis
Authors: Stantic Marina , Dong Lan‐Feng , Zobalova Renata , Prokopova Katerina , Neuzil Jiri
Published: November 2009

It is increasingly accepted that cancer stem cells (CSCs) are rather resistant to apoptosis to various inducers, including the immunological apoptogen TRAIL. Here we show that cancer cells with high expression of CD133, a marker that is often associated with CSCs, are resistant to TRAIL‐induced apoptosis, compared to their CD133‐low counterparts. We show that this resistance can be ascribed to the high expression of FLIP, an inhibitor of the extrinsic apoptotic pathway, in CD133‐high cells. Downregulation of FLIP by siRNA in CD133‐high cells sensitised them to TRAIL killing. Thus, CD133‐high cells may be resistant to TRAIL due to high expression of FLIP.
Downstream targets of altered sphingolipid metabolism in response to inhibition of ENOX2 by phenoxodiol
Authors: De Luca Thomas , Morré Dorothy M. , Bosneaga Elena , Morré D. James
Published: November 2009

Phenoxodiol, an ENOX2 inhibitor, alters cytosolic NADH levels to initiate a regulatory cascade linking sphingolipid metabolism and the PI3K/Akt pathway to programmed cell death. Specifically, the pyridine nucleotide products of plasma membrane redox, NAD+ and NADH, directly modulate in a recriprocal manner two key plasma membrane enzymes. NADH stimulation of sphingomyelinase and NADH inhibition of sphingosine kinase potentially lead to G1 arrest (increase in ceramide) and apoptosis (loss of sphingosine‐1‐phosphate). The findings link plasma membrane electron transport and the anticancer action of several clinically‐relevant anticancer agents targeted to ENOX2 such as phenoxodiol. Growth inhibition by phenoxodiol is unaffected by inhibitors of protein or mRNA synthesis. Findings with okadiaic acid, an inhibitor of serine/threonine phosphatases, suggest that hyperphosphorylation of intracellular substrates does not affect the action of phenoxodiol on ENOX2. Our findings and those of others are consistent with operation of the FAS signaling pathway of apoptosis and its suppression by sphingosine‐1‐phosphate. The prevailing hypothesis is that products of Akt activation, c‐FLIP and XIAP, which exhibit anticaspase activities to block FAS signaling when sphingosine‐1‐phospate is elevated, are down regulated to permit apoptosis when sphingosine‐1‐phosphate is decreased by inhibition of sphingosine kinase under conditions of elevated cytosolic NADH associated with anticancer drug inhibition of ENOX2.
Gendered dynamics of abuse and violence in families: considering the abusive household gender regime
Authors: Morris Anne
Published: November 2009

Despite evidence that child abuse and woman abuse often occur in the one household, responses to violence have generally focused on either women or children. The concept of an abusive household gender regime (AHGR) was developed through research on maternal alienation, the undermining of mother‐child relationships by perpetrators of violence. The concept of the AHGR allows a comprehensive understanding of the operation of gender and violence and the ways in which these impact on all household members and their relationships. An AHGR is characterised by perpetrators' imposition of a coercive web‐like regime on household members and the interlocking of many forms of abuse, which entrap victims. Perpetrators employ gendered constructions that demean women and advantage men. Resistance to the idea that fathers can be dangerous to their children bolsters the position of abusive fathers, and illustrates how there is minimisation or denial of men's responsibility for violence at all levels. Understanding gender, power and the AHGR allows the development of practice that combines child protection with woman protection, responds more holistically to the multi‐abuses perpetrated on family members and assists women and children together to recover from violence. Copyright © 2009 John Wiley & Sons, Ltd.
Characterization of molecular markers to assess cardiac cushions formation in Xenopus
Authors: Lee Young‐Hoon , Saint‐Jeannet Jean‐Pierre
Published: November 2009

The valves and septa of the mature heart are derived from the cardiac cushions, which develop from discrete swellings in two regions of developing heart tube: the atrioventricular (AV) canal and the ventricular outflow tract (OFT). In higher vertebrates, three distinct lineages contribute to the heart valves and septa, the endocardium, the myocardium, and the cardiac neural crest that will populate the cardiac jelly of the OFT. Very little is known about cardiac cushions development in amphibians. Here, we describe the expression of eight genes during key stages of cardiac cushion development in Xenopus. Among these genes, the Wnt antagonist Frzb1 and the transcription factors Xl‐Fli, Sox8, Sox9, and Sox10 are differentially expressed in the mesenchyme of the OFT and AV cushions. These genes can be used in combination with lineage‐tracing experiments to determine the embryonic origin of the cardiac cushions mesenchyme in Xenopus. Developmental Dynamics 238:3257–3265, 2009. © 2009 Wiley‐Liss, Inc.
The role of flooding on inter‐annual and seasonal variability of lake water chemistry, phytoplankton diatom communities and macrophyte biomass in the Slave River Delta (Northwest Territories, Canada)
Authors: Sokal Michael A. , Hall Roland I. , Wolfe Brent B.
Published: November 2009

Water chemistry, macrophyte biomass and planktonic diatom communities were monitored seasonally over 3 years (2003–2005) from six hydrologically diverse lakes to assess the role of river flooding on inter‐annual and seasonal variability of conditions in lakes of the Slave River Delta, Northwest Territories, Canada. Results indicate that river flooding was the dominant hydrological process controlling the temporal dynamics of the physical and chemical conditions, planktonic diatom communities and macrophyte biomass in lakes of the Slave River Delta. In the absence of river flooding, lakes had relatively high concentrations of nutrients and low concentrations of most ions, but when flooded, concentrations of nutrients decreased and ions increased. The physical and chemical conditions in frequently flooded and non‐flooded lakes were relatively stable from year to year, whereas lakes that were intermittently flooded fluctuated widely depending on whether or not they flooded. Spring flooding from the Slave River introduced planktonic, centric diatoms that persisted only for a few weeks in the water column before settling out. Non‐flooded lakes lacked planktonic diatoms. River flooding also reduced water transparency, which decreased macrophyte biomass, while lakes that did not flood exhibited higher macrophyte biomass and clear waters. This research provides insights into the factors that control the hydroecological variability of northern deltaic landscapes, and further improves our understanding of the complex interactions among hydrology, limnology and aquatic ecology, ultimately contributing to an improved scientific basis for future resource management decisions in the Slave River Delta and analogous systems. Copyright © 2009 John Wiley & Sons, Ltd.
Highly Selective Three‐Step Synthesis of Rhein in Chloroaluminate Molten Salt: Preclusion of the Hayashi Rearrangement
Authors: Gonnot Vanessa , Antheaume Cyril , Nicolas Marc , Mioskowski Charles , Baati Rachid
Published: November 2009

An expeditious, three‐step synthesis of rhein (2) was optimized starting from bis(N,N‐diethyl)‐5‐methoxybenzene‐1,3‐dicarboxamide. The key final step, involving deprotection/cyclization of ortho‐benzoylbenzoic acid 9 in acidic chloroaluminate molten salts, yielded the desired natural product with high selectivity and good overall yield by precluding the competitive Hayashi rearrangement.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
A New Kinetic‐Mechanistic Approach to Elucidate Formaldehyde Electrooxidation on Copper Electrode
Authors: Hasanzadeh Mohammad , Khalilzadeh Balal , Shadjou Nasrin , Karim‐Nezhad Ghasem , Saghatforoush Lotfali , Kazeman Isa , Abnosi Mohammad Hossein
Published: November 2009

Electrocatalytic oxidation of formaldehyde was investigated on copper electrode in alkaline solution. The process of oxidation involved and its kinetics were established by using cyclic voltammetry, chronoamperometry as well as steady state polarization measurements. In cyclic voltammetry (CV) studies, in the presence of formaldehyde the peak current increase of the oxidation of Cu(III) is followed by a decrease in the corresponding cathodic current. A new mechanism based on the electrochemical generation of Cu(III) active sites and their subsequent consumption by the formaldehyde in question was also investigated.
Alternative tilts for nonparametric option pricing
Authors: Haley M. Ryan , Walker Todd B.
Published: November 2009

This study generalizes the nonparametric approach to option pricing of Stutzer, M. (1996) by demonstrating that the canonical valuation methodology introduced therein is one member of the Cressie–Read family of divergence measures. Alhough the limiting distribution of the alternative measures is identical to the canonical measure, the finite sample properties are quite different. We assess the ability of the alternative divergence measures to price European call options by approximating the risk‐neutral, equivalent martingale measure from an empirical distribution of the underlying asset. A simulation study of the finite sample properties of the alternative measure changes reveals that the optimal divergence measure depends upon how accurately the empirical distribution of the underlying asset is estimated. In a simple Black–Scholes model, the optimal measure change is contingent upon the number of outliers observed, whereas the optimal measure change is a function of time to expiration in the stochastic volatility model of Heston, S. L. (1993). Our extension of Stutzer's technique preserves the clean analytic structure of imposing moment restrictions to price options, yet demonstrates that the nonparametric approach is even more general in pricing options than originally believed. © 2009 Wiley Periodicals, Inc. Jrl Fut Mark 30:983–1006, 2010
Cortical representation of verbs with optional complements: The theoretical contribution of fMRI
Authors: Shetreet Einat , Friedmann Naama , Hadar Uri
Published: November 2009

Verbs like “eat” are special in that they can appear both with a complement (e.g., “John ate ice‐cream”) and without a complement (“John ate”). How are such verbs with optional complements represented? This fMRI study attempted to provide neurally based constraints for the linguistic theory of the representation of verbs with optional complements. One linguistic approach suggests that the representation of these verbs in the lexicon includes two complementation frames (one with and one without the complement), similarly to verbs that allow two different types of complements (e.g., discover). Another approach assumes that only one frame is represented (with a complement) and, when the complement is omitted, the relevant thematic role is saturated, either lexically or syntactically. We compared the patterns of cortical activation of verbs with optional complements to verbs that take either one or two frames and to verbs with one or two complements. These comparisons—together with prior findings regarding the cortical activation related to the number of complementation frames and the number of complements—were used to decide between the theoretical approaches. We found support for the idea that verbs with optional complements have only one frame and that a lexical operation enables complement omission. We also used fMRI in the traditional manner and identified the fusiform gyrus and the temporo–parieto–occipital junction as the regions that participate in the execution of the omission and saturation of optional complements. Hum Brain Mapp, 2010. © 2009 Wiley‐Liss, Inc.