bluuebunny/crossref_metadata_2025_split huggingface dataset:
Y
Chromosome Evolution
Authors: Gvozdev Vladimir A 
Published: October 2009

Abstract

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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
Rapidly Evolving Regions of the Human Genome
Authors: Agarwal Subhash Mohan 
Published: October 2009

Abstract

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

Abstract
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

Abstract

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

Abstract
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

Abstract
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

AbstractX‐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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract

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.
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

AbstractBackgroundThe 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.MethodsA 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.ResultsAll 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.ConclusionsFarmers 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

AbstractBiological 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

AbstractThe 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

AbstractAnionic 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

AbstractThe 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

AbstractPeople 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

AbstractIn 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

AbstractThe 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

AbstractMany 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

AbstractOxidative 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.