bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Putative Stem Cell Markers, CD133 and CXCR4, in hTERT–Immortalized Primary Nonmalignant and Malignant Tumor-Derived Human Prostate Epithelial Cell Lines and in Prostate Cancer Specimens
Authors: Miki Jun , Furusato Bungo , Li Hongzhen , Gu Yongpeng , Takahashi Hiroyuki , Egawa Shin , Sesterhenn Isabell A. , McLeod David G. , Srivastava Shiv , Rhim Johng S. 
Published: April 2007

Abstract
Understanding normal and cancer stem cells may provide insight into the origin of and new therapeutics for prostate cancer. Normal and cancer stem cells in prostate have recently been identified with a CD44+/α2β1high/CD133+ phenotype. Stromal cell–derived factor-1 (SDF-1) and its receptor, CXCR4, have multiple essential functions, including homing of stem cells and metastasis of cancer cells. We show here that human telomerase reverse transcriptase (hTERT)-immortalized primary nonmalignant (RC-165N/hTERT) and malignant (RC-92a/hTERT) tumor-derived human prostate epithelial cell lines retain stem cell properties with a CD133+/CD44+/α2β1+/34βE12+/CK18+/p63−/androgen receptor (AR)−/PSA− phenotype. Higher CD133 expression was detected in the hTERT-immortalized cells than in primary prostate cells. These immortalized cells exhibited “prostaspheres” in nonadherent culture systems and also maintained higher CD133 expression. The CD133+ cells from these immortalized cell lines had high proliferative potential and were able to differentiate into AR+ phenotype. In three-dimensional culture, the CD133+ cells from RC-165N/hTERT cells produced branched structures, whereas the CD133+ cells from RC-92a/hTERT cells produced large irregular spheroids with less branched structures. SDF-1 induced, but anti-CXCR4 antibody inhibited, migration of CD133+ cells from RC-92a/hTERT cells, which coexpressed CXCR4. CXCR4/SDF-1 may sustain tumor chemotaxis in cancer stem cells. Furthermore, immunostaining of clinical prostate specimens showed that CD133 expression was detected in a subpopulation of prostate cancer cells and corresponded to the loss of AR. Expression of CXCR4 was also detected in CD133+ cancer cells. These novel in vitro models may offer useful tools for the study of the biological features and functional integration of normal and cancer stem cells in prostate. [Cancer Res 2007;67(7):3153–61]
Basophils are essential initiators of a novel type of chronic allergic inflammation
Authors: Obata Kazushige , Mukai Kaori , Tsujimura Yusuke , Ishiwata Kenji , Kawano Yohei , Minegishi Yoshiyuki , Watanabe Naohiro , Karasuyama Hajime 
Published: April 2007

AbstractBasophils represent less than 1% of peripheral blood leukocytes and have often been considered as minor and possibly redundant circulating mast cells. The recent finding that basophils readily generate large quantities of T helper 2 (Th2) cytokines such as IL-4 provided new insights into the possible role of basophils in allergic disorders and immunity to pathogens. However, in-depth studies on basophils, particularly their functions in vivo, have been hampered by the lack of appropriate animal models, such as mutant animals deficient only in basophils. Here, we established a mAb that reacted with mouse basophils and depleted them when administered in vivo. The mAb treatment of mice did not show any significant effect on classical allergic reactions such as passive cutaneous anaphylaxis and contact hypersensitivity. In contrast, it completely abolished the development of IgE-mediated chronic allergic dermatitis that is characterized by massive eosinophil infiltration, even though basophils accounted for only approximately 2% of the infiltrates. The treatment during the progression of the dermatitis resulted in drastic reduction in numbers of infiltrating eosinophils and neutrophils, concomitantly with elimination of basophils from the skin lesions. Thus, basophils play a pivotal role in the development of IgE-mediated chronic allergic inflammation, as an initiator rather than as an effector.
Modelling wear and crack initiation in rails
Authors: Franklin F J , Kapoor A 
Published: April 2007

Wear and crack initiation of steel rails is a problem of great significance to the railway industry. A high wear rate shortens the life of rails and the frequent rail replacement is expensive in terms not only of resources but also of track access time and delays affecting timetables. In addition, railhead profiles change gradually as the rails are worn and the greater the wear rate, the more often the rails need to be reground to maintain good train running performance. In contrast, a low wear rate means that cracks have time to develop in the plastically deformed rail steel and these may propagate deeper into the rails with potentially disastrous consequences. Finding the optimum combination of wear and grinding to maintain railhead profile and prevent cracks from growing is key to running a safe and cost-efficient railway. The large number of variables arising from track geometry, train dynamics, and wheel and rail profiles leads to wide variation in contact patch size and location. The two-dimensional model of ratcheting wear developed by Kapoor et al. has been developed to model the damage accumulation near the surface of the rail on the basis of a full three-dimensional contact stress distribution. Different rail steel microstructures can also be modelled and the effects of microstructure on wear and crack initiation are explored.
Experimental and theoretical investigation of railway wheel squeal
Authors: Hsu S S , Huang Z , Iwnicki S D , Thompson D J , Jones C J C , Xie G , Allen P D 
Published: April 2007

The tangential contact forces that arise at the interface between the wheel of a railway vehicle and the rail provide all the traction, braking, and guidance required by the vehicle. These forces are the result of microslip or creepage and can become unstable exciting vibration of the wheel, particularly at frequencies corresponding to the wheel's axial (and radial) modes. Although theories exist for predicting these creep forces and their relationship to creepages, most lack experimental verification in the characterization of the falling friction coefficient during unsteady squealing. This paper presents some new results from a project which aims to develop a complete, validated model of curve squeal noise generation accounting for friction characteristics, excitation due to unstable forces between the wheel and rail and vehicle dynamic behaviour. The model includes wheel and track dynamic response and acoustic radiation. As part of the project, a twin disc rig has been modified to provide experimental data for the validation of the model and measurements were made of the lateral force and dynamic response of the rollers due to varying amounts of lateral creepage during squealing. The main feature of the twin disc rig compared with previous research [1] is that the contact force measuring system measures the contact forces at the web of the rollers and therefore close to the contact patch and through a slipring arrangement enables the lateral vibration of both rollers in relation to squeal be measured with relative ease. In this paper, detailed descriptions of the twin disc rig and the test method developed are given. An outline of the squeal model is also presented. Results from the tests have been compared with the prediction from the squeal model and with available theories and showed good agreement.
Genetic and Environmental Influences on Plasma Homocysteine: Results from a Danish Twin Study
Authors: Bathum Lise , Petersen Inge , Christiansen Lene , Konieczna Agnieszka , Sørensen Thorkild IA , Kyvik Kirsten O 
Published: April 2007

Abstract
Background: Increased plasma homocysteine has been linked to many clinical conditions including atherosclerosis and ischemic stroke. We assessed the genetic and environmental influences on homocysteine in adult twins and tested the influence of 3 candidate polymorphisms.
Methods: Homocysteine was analyzed in 1206 healthy twins, who were genotyped for 3 polymorphisms: MTHFR 677C&gt;T, MTR 2756A&gt;G, and NNMT (dbSNP: rs694539). To perform quantitative trait linkage analysis of the MTHFR locus, the genotyping was supplemented with 2 genetic markers localized on each site of the MTHFR locus. The twin data were analyzed using biometric structural equation models as well as a combined association and linkage analysis in 2 age cohorts.
Results: Age, sex, and MTHFR genotype have a significant impact on homocysteine concentrations, whereas the other genotypes were not associated with homocysteine concentrations. The variance in homocysteine could be solely ascribed to additive genetic and nonshared environmental factors, with an estimated additive genetic proportion of total variation at age 18–39 years of 0.63 (95% CI, 0.53–0.71) and at age 40–65 years of 0.27 (95% CI, 0.10–0.41). The impact of the MTHFR locus is estimated to explain 53% (95% CI, 0.07–0.67) of the total phenotypic variation in persons 18–39 years old and 24% (95% CI, 0.00–0.39) in persons 40–65 years old, i.e., almost all additive genetic variance.
Conclusions: Homocysteine concentrations have a high heritability that decreases with age. The MTHFR gene locus is responsible for almost all the variation attributable to genetic factors, leaving very little influence of other genetic variations.
Morphological variation of two Alexandrium species responsible for paralytic shellfish poisoning in Southeast Asia
Authors: Lim Po-Teen , Leaw Chui-Pin , Ogata Takehiko 
Published: April 2007

Abstract
We examined in clonal cultures the morphological variation of two toxic dinoflagellates, Alexandrium tamiyavanichii and A. minutum, responsible for paralytic shellfish poisoning events in Southeast Asia. The Malaysian strain of A. tamiyavanichii had either a straight or oblique posterior margin on the first apical plate, and a triangular, square to trapezoid-shaped precingular part of the anterior sulcal plate. Morphological variability was also detected in the shape of the first apical plate, its connection to the apical pore, and the position of the ventral pore. In A. minutum, the Malaysian strains showed variation in the sixth precingular plate and the anterior sulcal plate. The length:width ratio of the sixth precingular plate varied from one to two. An anterior sulcal plate with a long left extension also occurred in both of the Malaysian strains. Several characters that have been extensively used in the identification of Alexandrium species have been proven quite variable.
Evolution of DNA Double-Strand Break Repair by Gene Conversion: Coevolution Between a Phage and a Restriction-Modification System
Authors: Yahara Koji , Horie Ryota , Kobayashi Ichizo , Sasaki Akira 
Published: April 2007

AbstractThe necessity to repair genome damage has been considered to be an immediate factor responsible for the origin of sex. Indeed, attack by a cellular restriction enzyme of invading DNA from several bacteriophages initiates recombinational repair by gene conversion if there is homologous DNA. In this work, we modeled the interaction between a bacteriophage and a bacterium carrying a restriction enzyme as antagonistic coevolution. We assume a locus on the bacteriophage genome has either a restriction-sensitive or a restriction-resistant allele, and another locus determines whether it is recombination/repair proficient or defective. A restriction break can be repaired by a co-infecting phage genome if one of them is recombination/repair proficient. We define the fitness of phage (resistant/sensitive and repair-positive/-negative) genotypes and bacterial (restriction-positive/-negative) genotypes by assuming random encounter of the genotypes, with given probabilities of single and double infections, and the costs of resistance, repair, and restriction. Our results show the evolution of the repair allele depends on $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(b_{1}/b_{0},\) \end{document}$ the ratio of the burst size $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(b_{1}\) \end{document}$ under damage to host cell physiology induced by an unrepaired double-strand break to the default burst size $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(b_{0}.\) \end{document}$ It was not until this effect was taken into account that the evolutionary advantage of DNA repair became apparent.
Genomewide Association Analysis in Diverse Inbred Mice: Power and Population Structure
Authors: McClurg Phillip , Janes Jeff , Wu Chunlei , Delano David L , Walker John R , Batalov Serge , Takahashi Joseph S , Shimomura Kazuhiro , Kohsaka Akira , Bass Joseph , Wiltshire Tim , Su Andrew I 
Published: April 2007

AbstractThe discovery of quantitative trait loci (QTL) in model organisms has relied heavily on the ability to perform controlled breeding to generate genotypic and phenotypic diversity. Recently, we and others have demonstrated the use of an existing set of diverse inbred mice (referred to here as the mouse diversity panel, MDP) as a QTL mapping population. The use of the MDP population has many advantages relative to traditional F2 mapping populations, including increased phenotypic diversity, a higher recombination frequency, and the ability to collect genotype and phenotype data in community databases. However, these methods are complicated by population structure inherent in the MDP and the lack of an analytical framework to assess statistical power. To address these issues, we measured gene expression levels in hypothalamus across the MDP. We then mapped these phenotypes as quantitative traits with our association algorithm, resulting in a large set of expression QTL (eQTL). We utilized these eQTL, and specifically cis-eQTL, to develop a novel nonparametric method for association analysis in structured populations like the MDP. These eQTL data confirmed that the MDP is a suitable mapping population for QTL discovery and that eQTL results can serve as a gold standard for relative measures of statistical power.
Adaptation of a Quantitative Trait to a Moving Optimum
Authors: Kopp Michael , Hermisson Joachim 
Published: April 2007

Abstract
We investigate adaptive evolution of a quantitative trait under stabilizing selection with a moving optimum. We characterize three regimes, depending on whether (1) the beneficial mutation rate, (2) the fixation time, or (3) the rate of environmental change is the limiting factor for adaptation. If the environment is rate limiting, mutations with a small phenotypic effect are prefered over large mutations, in contrast to standard theory.
A Novel Type of Sequence Variation: Multiple-Nucleotide Length Polymorphisms Discovered in the Bovine Genome
Authors: Jiang Zhihua , Wang Zeping , Kunej Tanja , Williams Galen A , Michal Jennifer J , Wu Xiao-Lin , Magnuson Nancy S 
Published: April 2007

Abstract
Three types of sequence variations—single-nucleotide polymorphisms (SNPs), insertions and deletions (indels), and short tandem repeats (STRs)—have been extensively reported in mammalian genomes. In this study, we discovered a novel type of sequence variation, i.e., multiple-nucleotide length polymorphisms (MNLPs) in bovine UCN3 (Urocortin 3) and its receptor CRHR2 (corticotropin-releasing hormone receptor 2) genes. Both MNLPs featured involvement of multiple-nucleotide length polymorphisms (5–18 bases), low sequence identity, and 1.7- to 11-fold changes in promoter activity between two alleles. Therefore, this novel genetic complexity would contribute significantly to the evolutionary, functional, and phenotypic complexity of genomes within or among species.
Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice
Authors: Osato Naoki , Suzuki Yoshiyuki , Ikeo Kazuho , Gojobori Takashi 
Published: April 2007

Abstract
For a significant fraction of mRNAs, their expression is regulated by other RNAs, including cis natural antisense transcripts (cis-NATs) that are complementary mRNAs transcribed from opposite strands of DNA at the same genomic locus. The regulatory mechanism of mRNA expression by cis-NATs is unknown, although a few possible explanations have been proposed. To understand this regulatory mechanism, we conducted a large-scale analysis of the currently available data and examined how the overlapping arrangements of cis-NATs affect their expression level. Here, we show that for both human and mouse the expression level of cis-NATs decreases as the length of the overlapping region increases. In particular, the proportions of the highly expressed cis-NATs in all cis-NATs examined were ∼36 and 47% for human and mouse, respectively, when the overlapping region was &lt;200 bp. However, both proportions decreased to virtually zero when the overlapping regions were &gt;2000 bp in length. Moreover, the distribution of the expression level of cis-NATs changes according to different types of the overlapping pattern of cis-NATs in the genome. These results are consistent with the transcriptional collision model for the regulatory mechanism of gene expression by cis-NATs.
Inorganic Phosphate Deprivation Causes tRNA Nuclear Accumulation via Retrograde Transport inSaccharomyces cerevisiae
Authors: Hurto Rebecca L , Tong Amy Hin Yan , Boone Charles , Hopper Anita K 
Published: April 2007

AbstractNuclear export of tRNA is an essential eukaryotic function, yet the one known yeast tRNA nuclear exporter, Los1, is nonessential. Moreover recent studies have shown that tRNAs can move retrograde from the cytosol to the nucleus by an undefined process. Therefore, additional gene products involved in tRNA nucleus–cytosol dynamics have yet to be identified. Synthetic genetic array (SGA) analysis was employed to identify proteins involved in Los1-independent tRNA transport and in regulating tRNA nucleus–cytosol distribution. These studies uncovered synthetic interactions between los1Δ and pho88Δ involved in inorganic phopshate uptake. Further analysis revealed that inorganic phosphate deprivation causes transient, temperature-dependent nuclear accumulation of mature cytoplasmic tRNA within nuclei via a Mtr10- and retrograde-dependent pathway, providing a novel connection between tRNA subcellular dynamics and phosphate availability.
A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium
Authors: Guo Wangzhen , Cai Caiping , Wang Changbiao , Han Zhiguo , Song Xianliang , Wang Kai , Niu Xiaowei , Wang Cheng , Lu Keyu , Shi Ben , Zhang Tianzhen 
Published: April 2007

Abstract
The mapping of functional genes plays an important role in studies of genome structure, function, and evolution, as well as allowing gene cloning and marker-assisted selection to improve agriculturally important traits. Simple sequence repeats (SSRs) developed from expressed sequence tags (ESTs), EST–SSR (eSSR), can be employed as putative functional marker loci to easily tag corresponding functional genes. In this paper, 2218 eSSRs, 1554 from G. raimondii-derived and 754 from G. hirsutum-derived ESTs, were developed and used to screen polymorphisms to enhance our backbone genetic map in allotetraploid cotton. Of the 1554 G. raimondii-derived eSSRs, 744 eSSRs were able to successfully amplify polymorphisms between our two mapping parents, TM-1 and Hai7124, presenting a polymorphic rate of 47.9%. However, only a 23.9% (159/754) polymorphic rate was produced from G. hirsutum-derived eSSRs. No relationship was observed between the level of polymorphism, motif type, and tissue origin, but the polymorphism appeared to be correlated with repeat type. After integrating these new eSSRs, our enhanced genetic map consists of 1790 loci in 26 linkage groups and covers 3425.8 cM with an average intermarker distance of 1.91 cM. This microsatellite-based, gene-rich linkage map contains 71.96% functional marker loci, of which 87.11% are eSSR loci. There were 132 duplicated loci bridging 13 homeologous At/Dt chromosome pairs. Two reciprocal translocations after polyploidization between A2 and A3, and between A4 and A5, chromosomes were further confirmed. A functional analysis of 975 ESTs producing 1122 eSSR loci tagged in the map revealed that 60% had clear BLASTX hits (&lt;1e−10) to the Uniprot database and that 475 were associated mainly with genes belonging to the three major gene ontology categories of biological process, cellular component, and molecular function; many of the ESTs were associated with two or more category functions. The results presented here will provide new insights for future investigations of functional and evolutionary genomics, especially those associated with cotton fiber improvement.
Stepping-Stone Spatial Structure Causes Slow Decay of Linkage Disequilibrium and Shifts the Site Frequency Spectrum
Authors: De Arkendra , Durrett Richard 
Published: April 2007

Abstract
The symmetric island model with D demes and equal migration rates is often chosen for the investigation of the consequences of population subdivision. Here we show that a stepping-stone model has a more pronounced effect on the genealogy of a sample. For samples from a small geographical region commonly used in genetic studies of humans and Drosophila, there is a shift of the frequency spectrum that decreases the number of low-frequency-derived alleles and skews the distribution of statistics of Tajima, Fu and Li, and Fay and Wu. Stepping-stone spatial structure also changes the two-locus sampling distribution and increases both linkage disequilibrium and the probability that two sites are perfectly correlated. This may cause a false prediction of cold spots of recombination and may confuse haplotype tests that compute probabilities on the basis of a homogeneously mixing population.
Toxicity of 5% Rotenone to Nonindigenous Asian Swamp Eels
Authors: Schofield Pamela J. , Nico Leo G. 
Published: April 2007

Abstract
Our primary goal was to determine whether rotenone would be a useful control against introduced populations of Asian swamp eels (family Synbranchidae, genus Monopterus). We report the results of a laboratory experiment comparing the efficacy of various rotenone concentrations (1, 2, 4, and 8 mg of 5% liquid rotenone/L of water) in killing nonindigenous swamp eels of various sizes (1–350 g) from the three known Florida populations. Although most small swamp eels were killed at concentrations of 2 and 4 mg/L, 100% mortality of adult swamp eels was achieved only at 8 mg/L. We conclude that the effective use of rotenone to control established Florida swamp eel populations would be difficult, based on the relatively high concentration of rotenone needed to kill swamp eels; the complexity of the swamp eel's habitat; and our observations of the species' habitat use and behavior, including its widespread distribution and life history characteristics (e.g., burrowing and overland movement) that enhance its invasion and survival in multiple environments. Nevertheless, control of swamp eels may be achieved in certain situations. A combination of rotenone and electroshocking may be an effective way to eradicate swamp eels from small water bodies and to control populations in larger habitats. However, we are cautious in this recommendation and provide details related to the technical aspects of this type of strategy and caveats related to the toxicity of the chemical.