bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rate-Controlled Lateral-load Pile Tests Using a Robotic Manipulator in Centrifuge
Authors: Kong LG , Zhang LM 
Published: October 2006

Abstract
Robotic manipulators, as a new facility for centrifuge modeling, can provide a platform to carry out complex in-flight simulation of geotechnical problems. In this study, a four-axis robotic manipulator was employed to conduct a series of laterally-loaded pile tests in sand. Four model piles were installed into a sand bed and laterally loaded at different loading rates consecutively without stopping the centrifuge, which accordingly maximized consistency of the soil sample among the tests. Tests in both loose sand and dense sand were conducted. Detailed information of the test devices and procedures of soil sample preparation and load testing is described in this paper. The test results, including horizontal force-displacement curves, bending moment distributions, relationships between lateral resistance and loading rates, and p-y curves derived from the measured bending moment distributions, are presented. In addition, the effects of loading rate and ground surface are discussed based on the test results. It is found that, under the investigated conditions, loading rate has little effect on the horizontal resistance at specified displacements, but has significant effects on the bending moment and soil reaction distributions. The ground surface also has an effect on the behavior of the laterally-loaded piles. A simple modification method is used to consider the effect of ground surface on p-y curves at shallow depths.
Molecular Analysis, Cytogenetics and Fertility of Introgression Lines From Transgenic Wheat to Aegilops cylindrica Host
Authors: Schoenenberger Nicola , Guadagnuolo Roberto , Savova-Bianchi Dessislava , Küpfer Philippe , Felber François 
Published: October 2006

Abstract
Natural hybridization and backcrossing between Aegilops cylindrica and Triticum aestivum can lead to introgression of wheat DNA into the wild species. Hybrids between Ae. cylindrica and wheat lines bearing herbicide resistance (bar), reporter (gus), fungal disease resistance (kp4), and increased insect tolerance (gna) transgenes were produced by pollination of emasculated Ae. cylindrica plants. F1 hybrids were backcrossed to Ae. cylindrica under open-pollination conditions, and first backcrosses were selfed using pollen bags. Female fertility of F1 ranged from 0.03 to 0.6%. Eighteen percent of the sown BC1s germinated and flowered. Chromosome numbers ranged from 30 to 84 and several of the plants bore wheat-specific sequence-characterized amplified regions (SCARs) and the bar gene. Self fertility in two BC1 plants was 0.16 and 5.21%, and the others were completely self-sterile. Among 19 BC1S1 individuals one plant was transgenic, had 43 chromosomes, contained the bar gene, and survived glufosinate treatments. The other BC1S1 plants had between 28 and 31 chromosomes, and several of them carried SCARs specific to wheat A and D genomes. Fertility of these plants was higher under open-pollination conditions than by selfing and did not necessarily correlate with even or euploid chromosome number. Some individuals having supernumerary wheat chromosomes recovered full fertility.
An Arabidopsis Basic Helix-Loop-Helix Leucine Zipper Protein Modulates Metal Homeostasis and Auxin Conjugate Responsiveness
Authors: Rampey Rebekah A , Woodward Andrew W , Hobbs Brianne N , Tierney Megan P , Lahner Brett , Salt David E , Bartel Bonnie 
Published: October 2006

Abstract
The plant hormone auxin can be regulated by formation and hydrolysis of amide-linked indole-3-acetic acid (IAA) conjugates. Here, we report the characterization of the dominant Arabidopsis iaa–leucine resistant3 (ilr3-1) mutant, which has reduced sensitivity to IAA–Leu and IAA–Phe, while retaining wild-type responses to free IAA. The gene defective in ilr3-1 encodes a basic helix-loop-helix leucine zipper protein, bHLH105, and the ilr3-1 lesion results in a truncated product. Overexpressing ilr3-1 in wild-type plants recapitulates certain ilr3-1 mutant phenotypes. In contrast, the loss-of-function ilr3-2 allele has increased IAA–Leu sensitivity compared to wild type, indicating that the ilr3-1 allele confers a gain of function. Microarray and quantitative real-time PCR analyses revealed five downregulated genes in ilr3-1, including three encoding putative membrane proteins similar to the yeast iron and manganese transporter Ccc1p. Transcript changes are accompanied by reciprocally misregulated metal accumulation in ilr3-1 and ilr3-2 mutants. Further, ilr3-1 seedlings are less sensitive than wild type to manganese, and auxin conjugate response phenotypes are dependent on exogenous metal concentration in ilr3 mutants. These data suggest a model in which the ILR3/bHLH105 transcription factor regulates expression of metal transporter genes, perhaps indirectly modulating IAA-conjugate hydrolysis by controlling the availability of metals previously shown to influence IAA–amino acid hydrolase protein activity.
The Association Among Gene Expression Responses to Nine Abiotic Stress Treatments inArabidopsis thaliana
Authors: Swindell William R 
Published: October 2006

AbstractThe identification and analysis of genes exhibiting large expression responses to several different types of stress may provide insights into the functional basis of multiple stress tolerance in plant species. This study considered whole-genome transcriptional profiles from Arabidopsis thaliana root and shoot organs under nine abiotic stress conditions (cold, osmotic stress, salt, drought, genotoxic stress, ultraviolet light, oxidative stress, wounding, and high temperature) and at six different time points of stress exposure (0.5, 1, 3, 6, 12, and 24 hr). In roots, genomewide correlations between transcriptional responses to different stress treatments peaked following 1 hr of stress exposure, while in shoots, correlations tended to increase following 6 hr of stress exposure. The generality of stress responses at the transcriptional level was therefore time and organ dependent. A total of 67 genes were identified as exhibiting a statistically significant pattern of gene expression characterized by large transcriptional responses to all nine stress treatments. Most genes were identified from early to middle (1–6 hr) time points of stress exposure. Analysis of this gene set indicated that cell rescue/defense/virulence, energy, and metabolism functional classes were overrepresented, providing novel insight into the functional basis of multiple stress tolerance in Arabidopsis.
Structure–Function Analysis of Delta Trafficking, Receptor Binding and Signaling in Drosophila
Authors: Parks Annette L , Stout Jane R , Shepard Scott B , Klueg Kristin M , Dos Santos Ana A , Parody Todd R , Vaskova Martina , Muskavitch Marc A T 
Published: October 2006

AbstractThe transmembrane proteins Delta and Notch act as ligand and receptor in a conserved signaling pathway required for a variety of cell fate specification events in many organisms. Binding of Delta to Notch results in a proteolytic cascade that releases the Notch intracellular domain, allowing it to participate in transcriptional activation in the nucleus. Recent research has implicated the endocytic and ubiquitylation machinery as essential components of Delta–Notch signaling. Our analysis of chimeric and missense Delta variants has delineated a number of structural requirements for Delta trafficking, receptor binding, and signaling. We find that while the Delta N-terminal domain is necessary and sufficient for binding to Notch, the integrity of the epidermal-growth-factor-like repeat (ELR) 2 is also required for Notch binding. Screening of 117 Delta mutant lines for proteins that exhibit aberrant subcellular trafficking has led to the identification of 18 Delta alleles (DlTD alleles) that encode “trafficking-defective” Delta proteins. We find, unexpectedly, that many DlTD alleles contain missense mutations in ELRs within the Delta extracellular domain. Finally, we find that two DlTD alleles contain lysine missense mutations within the Delta intracellular domain (DeltaICD) that may identify residues important for DeltaICD mono-ubiquitylation and subsequent Delta endocytosis and signaling.
Molecular Diversity After a Range Expansion in Heterogeneous Environments
Authors: Wegmann Daniel , Currat Mathias , Excoffier Laurent 
Published: October 2006

Abstract
Recent range expansions have probably occurred in many species, as they often happen after speciation events, after ice ages, or after the introduction of invasive species. While it has been shown that range expansions lead to patterns of molecular diversity distinct from those of a pure demographic expansion, the fact that many species do live in heterogeneous environments has not been taken into account. We develop here a model of range expansion with a spatial heterogeneity of the environment, which is modeled as a gamma distribution of the carrying capacities of the demes. By allowing temporal variation of these carrying capacities, our model becomes a new metapopulation model linking ecological parameters to molecular diversity. We show by extensive simulations that environmental heterogeneity induces a loss of genetic diversity within demes and increases the degree of population differentiation. We find that metapopulations with low average densities are much more affected by environmental heterogeneity than metapopulations with high average densities, which are relatively insensitive to spatial and temporal variations of the environment. Spatial heterogeneity is shown to have a larger impact on genetic diversity than temporal heterogeneity. Overall, temporal heterogeneity and local extinctions are not found to leave any specific signature on molecular diversity that cannot be produced by spatial heterogeneity.
Double-Strand Break Repair in Bacteriophage T4: Recombination Effects of 3′–5′ Exonuclease Mutations
Authors: Shcherbakov Victor P , Kudryashova E A , Shcherbakova T S , Sizova S T , Plugina L A 
Published: October 2006

Abstract
The role of 3′–5′ exonucleases in double-strand break (DSB)-promoted recombination was studied in crosses of bacteriophage T4, in which DSBs were induced site specifically within the rIIB gene by SegC endonuclease in the DNA of only one of the parents. Frequency of rII+ recombinants was measured in two-factor crosses of the type i × ets1, where ets1 designates an insertion in the rIIB gene carrying the cleavage site for SegC and i's are rIIB or rIIA point mutations located at various distances (12–2040 bp) from the ets1 site. The frequency/distance relationship was obtained in crosses of the wild-type phage and dexA1 (deficiency in deoxyribonuclease A), D219A (deficiency in the proofreading exonuclease of DNA polymerase), and tsL42 (antimutator allele of DNA polymerase) mutants. In all the mutants, recombinant frequency in crosses with the i-markers located at 12 and 33 bp from ets1 was significantly enhanced, implying better preservation of 3′-terminal sequences at the ends of the broken DNA. The effects of dexA1 and D219A were additive, suggesting an independent action of the corresponding nucleases in the DSB repair pathway. The recombination enhancement in the dexA1 mutant was limited to short distances (&lt;100 bp from ets1), whereas in the D219A mutant a significant enhancement was seen at all the tested distances. From the character of the frequency/distance relationship, it is inferred that the synthesis-dependent strand-annealing pathway may operate in the D219A mutant. The recombination-enhancing effect of the tsL42 mutation could be explained by the hypothesis that the antimutator 43Exo removes a shorter stretch of paired nucleotides than the wild-type enzyme does during hydrolysis of the unpaired terminus in the D-loop intermediate. The role of the proofreading exonuclease in the formation of a robust replicative fork is discussed.
Long-Term Culturing of Undifferentiated Embryonic Stem Cells in Conditioned Media and Three-Dimensional Fibrous Matrices Without Extracellular Matrix Coating
Authors: Ouyang Anli , Ng Robin , Yang Shang-Tian 
Published: October 2006

Abstract
ESCs have unlimited proliferation potential and capability to differentiate into all tissue types. They are ideal cell sources for tissue engineering and cell therapy, but their supplies are limited. Current in vitro ESC cultures are carried out in tissue flasks with the surface precoated with extracellular matrix (ECM) proteins. T-flask cultures also require frequent subculturing because their limited surface area cannot support long-term growth of ESCs. In this work, ECM coating and frequent subculturing required in two-dimensional (2D) cultures were circumvented by culturing murine ESCs in three-dimensional (3D) polyethylene terephthalate (PET) fibrous matrices. Also, media conditioned with STO fibroblast cells were used to replace leukemia inhibitory factor and to effectively maintain the pluripotency of murine ESCs in a long-term static culture. However, the lactic acid present in the conditioned medium could inhibit ESC growth and induce spontaneous differentiation when its concentration exceeded 1.5 g/l. In addition, the 3D static culture could be limited by oxygen, which was depleted in the long-term culture when cell density in the matrix was high. However, these problems can be alleviated in dynamic culture with improved oxygen transfer and continuous media perfusion. The matrix pore size also had profound effects on ESCs. The smaller-pore (30–60 μm) matrix gave a higher proliferation rate and Oct-4 and stage specific embryonic antigen-1 expressions. Overall, the 3D culturing method is superior to the 2D culture method and can provide an economical way to mass-produce undifferentiated ESCs in uncoated matrices and conditioned media.
Clonogenic Endothelial Progenitor Cells Are Sensitive to Oxidative Stress
Authors: Ingram David A. , Krier Theresa R. , Mead Laura E. , McGuire Colleen , Prater Daniel N. , Bhavsar Janak , Saadatzadeh M. Reza , Bijangi-Vishehsaraei Khadijeh , Li Fang , Yoder Mervin C. , Haneline Laura S. 
Published: October 2006

Abstract
Endothelial progenitor cells (EPCs) circulate in the peripheral blood and reside in blood vessel walls. A hierarchy of EPCs exists where progenitors can be discriminated based on their clonogenic potential. EPCs are exposed to oxidative stress during vascular injury as residents of blood vessel walls or as circulating cells homing to sites of neovascularization. Given the links between oxidative injury, endothelial cell dysfunction, and vascular disease, we tested whether EPCs were sensitive to oxidative stress using newly developed clonogenic assays. Strikingly, in contrast to previous reports, we demonstrate that the most proliferative EPCs (high proliferative potential-endothelial colony-forming cells and low proliferative potential-endothelial colony-forming cells) had decreased clonogenic capacity after oxidant treatment. In addition, EPCs exhibited increased apoptosis and diminished tube-forming ability in vitro and in vivo in response to oxidative stress, which was directly linked to activation of a redox-dependent stress-induced kinase pathway. Thus, this study provides novel insights into the effect of oxidative stress on EPCs. Furthermore, this report outlines a framework for understanding how oxidative injury leads to vascular disease and potentially limits the efficacy of transplantation of EPCs into ischemic tissues enriched for reactive oxygen species and oxidized metabolites.
Concise Review: Epigenetic Mechanisms Contribute to Pluripotency and Cell Lineage Determination of Embryonic Stem Cells
Authors: Gan Qiong , Yoshida Tadashi , McDonald Oliver G. , Owens Gary K. 
Published: October 2006

Abstract
Epigenetic mechanisms, such as histone modifications and DNA methylation, have been shown to play a key role in the regulation of gene transcription. Results of recent studies indicate that a novel “bivalent” chromatin structure marks key developmental genes in embryonic stem cells (ESCs), wherein a number of untranscribed lineage-control genes, such as Sox1, Nkx2-2, Msx1, Irx3, and Pax3, are epigenetically modified with a unique combination of activating and repressive histone modifications that prime them for potential activation (or repression) upon cell lineage induction and differentiation. However, results of these studies also showed that a subset of lineage-control genes, such as Myf5 and Mash1, were not marked by these histone modifications, suggesting that distinct epigenetic mechanisms might exist for lineage-control genes in ESCs. In this review article, we summarize evidence regarding possible mechanisms that control these unique histone modifications at lineage-control gene loci in ESCs and consider their possible contribution to ESC pluripotency. In addition, we propose a novel “histone modification pulsing” model wherein individual pluripotent stem cells within the inner cell mass of blastocysts undergo transient asynchronous histone modifications at these developmental gene loci, thereby conferring differential responsiveness to environmental cues and morphogenic gradients important for cell lineage determination. Finally, we consider how these rapid histone modification exchanges become progressively more stable as ESCs undergo differentiation and maturation into specialized cell lineages.
Identification ofCXCR4as a New Nitric Oxide-Regulated Gene in Human CD34+ Cells
Authors: Zhang Yanyan , Wittner Monika , Bouamar Hakim , Jarrier Peggy , Vainchenker William , Louache Fawzia 
Published: October 2006

AbstractAs an intracellular second messenger, nitric oxide (NO) is increasingly implicated in the control of transcriptional machinery and gene expression. Here, we show that cell surface expression of CXCR4 on CD34+ cells was increased in a dose- and time-dependent manner in response to NO donors. Augmented surface expression was correlated with an increase in CXCR4 mRNA level. A specific NO scavenger prevented the elevation in CXCR4 mRNA caused by NO donors, suggesting a direct signaling action mediated by NO on CXCR4 transcription. NO treatment had no significant effect on CXCR4 mRNA stability. However, induction of CXCR4 mRNA by NO was still observed in conditions in which initiation of translation was inhibited, suggesting that the NO effect must be mediated by a pre-existing protein. CXCR4 mRNA induction did not involve cGMP (guanosine 3′, 5′-cyclic monophosphate) generation but was most likely mediated via oxidation of intracellular protein thiols. Finally, CD34+ cells pretreated with NO donors exhibited an increased chemotactic response. This study demonstrates that the NO pathway can modulate CXCR4 expression in human CD34+ cells and suggests that NO may play a critical role in the trafficking of hematopoietic progenitors.
Update on Capecitabine in Colorectal Cancer
Authors: Schmoll Hans-Joachim , Arnold Dirk 
Published: October 2006

Learning Objectives
After completing this course, the reader will be able to: Discuss the potential use of oral capecitabine versus i.v. 5-FU in the treatment of colorectal cancer.Explain the evolving role of capecitabine in combination with novel, targeted therapeutics.Describe the role of capecitabine in combination with radiation therapy.
Access and take the CME test online and receive 1 AMA PRA Category 1 Credit™ at CME.TheOncologist.com
Referral to Medical Oncology: A Crucial Step in the Treatment of Older Patients with Stage III Colon Cancer
Authors: Luo RuiLi , Giordano Sharon H. , Freeman Jean L. , Zhang Dong , Goodwin James S. 
Published: October 2006

Learning Objectives
After completing this course, the reader will be able to: Identify the predictors of seeing a medical oncologist for older colon cancer patients.Discuss the association between seeing a medical oncologist and chemotherapy use in stage III colon cancer.Outline the clinical implications for colon cancer care.
Access and take the CME test online and receive 1 AMA PRA Category 1 Credit™ at CME.TheOncologist.com
Therapy for Metastatic Colorectal Cancer
Authors: Goldberg Richard M. 
Published: October 2006

Learning Objectives
After completing this course, the reader will be able to: Compare toxicity profiles among combination chemotherapy programs for colorectal cancer.Identify median survival times for chemotherapy programs for colorectal cancer.Discuss the new Intergroup trial schema and the rationale behind the study.
Access and take the CME test online and receive 1 AMA PRA Category 1 Credit™ at CME.TheOncologist.com
The Present and Future of Angiogenesis-Directed Treatments of Colorectal Cancer
Authors: O'Dwyer Peter J. 
Published: October 2006

Learning Objectives
After completing this course, the reader will be able to: Discuss the current status of clinical trials targeting angiogenesis in colorectal cancer.Identify the potential different mechanisms whereby antiangiogenic agents may interact with cytotoxic chemotherapy.Define potential mechanisms for resistance and sensitivity to antiangiogenic agents in colorectal cancer.
Access and take the CME test online and receive 1 AMA PRA Category 1 Credit™ at CME.TheOncologist.com
Nasal Levels of Nitric Oxide as an Outcome Variable in Allergic Upper Respiratory Tract Disease: Influence of Atopy and Hayfever on nNO
Authors: Moody Alison , Fergusson Wendy , Wells Athol , Bartley James , Kolbe John 
Published: October 2006

Background The role of nasal levels of nitric oxide (nNO) as noninvasive marker of inflammation and as an outcome variable in allergic upper respiratory tract disease has not been defined. Our aim is to determine in patients with perennial allergic rhinitis (i) whether nNO is elevated, (ii) whether increased nNO is correlated with upper respiratory tract symptoms (discrimination), and (iii) whether changes in symptom scores are associated with changes in nNO levels (responsiveness). Methods Subjects (n = 38) with perennial rhinitis were studied weekly for 3 weeks. At each visit they completed a validated symptom questionnaire and had expired NO and nNO measured. Results Nasal NO levels were higher in those allergic to house-dust mite and cat. Nasal NO levels in subjects with perennial rhinitis were not elevated compared with non-atopic asymptomatic subjects. The intra-week reproducibility of nNO measurements was poor. There was no relationship between the symptom scores and nasal NO levels (discrimination). When analysis was confined to nasal symptoms, a weak but negative correlation was identified. Changes in symptom scores from week to week were not correlated with changes in nNO levels (responsiveness). Conclusions Nasal NO levels were not elevated in subjects with perennial rhinitis, and nNO levels were neither discriminatory nor responsive. The measurement of nNO therefore appears not to be a useful marker of disease activity in subjects with allergic rhinitis.