bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Profiling of Signaling Networks: Study of Breast Cancer Stem Cells and Potential Regulation
Authors: Wang Hongxia , Huang Mingzhu , Zhang David Y. , Zhang Fengchun 
Published: June 2011

Abstract
There is overwhelming evidence that breast cancer may be driven by a small subset of breast cancer stem cells (BCSCs) that display stem/progenitor cell properties. In the present study, we identified the rare population of BCSCs, the so-called side population (SP) cells, using flow cytometry. Then, we used microarray analysis to study the differential gene expression profiles between SP and non-SP cells. Sixty-three probe sets showed a more than fourfold difference. Next, we compared the levels of proteins with Pathway Array using 154 antibodies, focusing on the proteins and phosphorylation sites that differed among SP cells, malignant mammary cells, and breast cancer tissues. Our results revealed that 40 proteins and phosphorylation sites were more than 1.5-fold different in SP cells than in non-SP cells. By comparing SP cells, MCF7 cells, and nontumorigenic MCF10A cells, we found 12 proteins that were significantly upregulated in SP cells; these proteins—cAMP-response element binding protein (CREB), cyclic AMP-dependent transcription factor 1, mesothelin, thyroid transcription factor 1, phosphorylated (p)-focal adhesion kinase, p38, Bad, p-CREB, p-protein kinase C (PKC)δ, Wee1, cell division cycle 42, and Twist—were more likely to play important roles in the signaling regulation of BCSCs. Further, 16 proteins and phosphoproteins showed differential expression in SP cells and tumor tissues. β-catenin, p-PKCα, and p-CREB were upregulated in both SP cells and breast tumors. Finally, we filtered the differential expression proteins, summarized the pathway interactions of these proteins, and rebuilt Path-Net in order to determine molecular mechanisms and core regulators. This process will allow us to identify signature patterns and mechanisms of signaling networks in BCSCs.
Potential Prognostic Biomarkers for Bone Metastasis from Hepatocellular Carcinoma
Authors: Xiang Zuo-Lin , Zeng Zhao-Chong , Tang Zhao-You , Fan Jia , He Jian , Zeng Hai-Ying , Zhu Xiao-Dong 
Published: June 2011

Abstract

Background.
Hepatocellular carcinoma (HCC) most commonly develops in patients who have a viral infection, especially in the case of hepatitis B virus (HBV), and in patients with a chronic liver disease. HCC patients with bone metastasis (BM) suffer from pain and other symptoms that significantly reduce their quality of life. Identification of patients who are at high risk for BM after undergoing potentially curative treatment for HCC remains challenging. Here, we aimed to identify HCC BM-related genes and proteins to establish prediction biomarkers.

Methods.
RNA was extracted from 48 pairs of intratumoral and peritumoral formalin-fixed, paraffin-embedded tissue from HCC patients with and without BM. A cDNA-mediated annealing, selection, extension and ligation assay containing 502 cancer-related genes was used to identify novel BM-associated genes. An additional independent study with 350 HCC patients who had undergone hepatectomy was conducted to evaluate the expression of candidate genes at the protein level using immunohistochemistry on tissue microarrays (TMAs). Of the 350 patients, 273 (78.0%) were infected with HBV.

Results.
Seven intratumoral genes and 17 peritumoral genes were overexpressed in patients with BM, whereas 15 intratumoral genes and 28 peritumoral genes were underexpressed in patients with BM. We selected the following four genes for further analysis because they were differentially expressed in the cancer gene-specific microarray and were previously reported to be associated with BM: connective tissue growth factor (CTGF), matrix metalloproteinase-1 (MMP-1), transforming growth factor β1 (TGF-β1), and interleukin-11 (IL-11). We assessed the protein expression of these selected genes using immunohistochemistry on TMAs including 350 HCC patient specimens. We determined that expression of intratumoral CTGF, intratumoral IL-11, and peritumoral MMP-1 were independent prognostic factors for developing BM in HCC patients. Combining intratumoral CTGF and IL-11 expression was also an independent risk factor for BM development.

Conclusions.
Sixty-seven genes were differentially expressed in HCC patients with and without BM. High intratumoral CTGF, positive IL-11, and high peritumoral MMP-1 expression were associated with BM after hepatectomy. Intratumoral CTGF expression combined with IL-11 expression may serve as a useful predictive biomarker for HCC BM.
Linking Policy to Statistical Uncertainty in Air Pollution Damages
Authors: Muller Nicholas Z 
Published: June 2011

Abstract
This study uses Monte Carlo analysis to characterize the uncertainty associated with per-ton damage estimates for 565 electric generating units (EGUs) in the contiguous United States (U.S.) This analysis focuses on damage estimates produced by an Integrated Assessment Model (IAM) for emissions of five local air pollutants: sulfur dioxide (SO2), nitrogen oxides (NOx), volatile organic compounds (VOCs), ammonia (NH3), and fine particulate matter (PM2.5). For each power plant and pollutant, the Monte Carlo procedure yields an empirical distribution for the damage per ton, or marginal damage. The paper links uncertainty in marginal damages to air pollution policy in two ways. First, the paper characterizes uncertainty in the magnitude of the marginal damages which is relevant to policymakers in determining the stringency of pollution controls. Second, the paper explores uncertainty in the relative damages across power plants. Relative damages are important if policymakers elect to design efficient regulations that vary in stringency according to where emissions are released. The empirical section of the paper finds that the marginal damage distributions are positively skewed and they are more variable for sources in urban areas than rural locations. The paper finds that uncertainty in three input parameters has the greatest impact on uncertainty in the magnitude of damages: the adult mortality dose-response parameter, the mortality valuation parameter, and air quality modeling. The analysis also finds that for each pollutant except for NOx only uncertainty in air quality modeling impacts efficient trading ratios calibrated to each firm's marginal damages.
Conditions for strong Morita equivalence of partially ordered semigroups
Authors: Tart Lauri 
Published: June 2011

Abstract
We investigate when a partially ordered semigroup (with various types of local units) is strongly Morita equivalent to a posemigroup from a given class of partially ordered semigroups. Necessary and sufficient conditions for such equivalence are obtained for a series of well-known classes of posemigroups. A number of sufficient conditions for several classes of naturally ordered posemigroups are also provided.
Erratum to: “Degradation of coatings based on 310S steel doped with Al and Ir additives by the scratch test” by Barbara Kucharska
Authors: Kucharska Barbara 
Published: June 2011

Abstract
The original version of the article was published in Central European Journal of Physics 9, 1122–1130 (2011), DOI: 10.2478/s11534-011-0005-8. Unfortunately, the original version of this article contains a mistake in Tab. 2. Here we display the corrected version of this table.
New approach to regeneration of an ionic liquid containing solvent by molecular distillation
Authors: Blahušiak Marek , Schlosser Štefan , Cvengroš Ján , Marták Ján 
Published: June 2011

AbstractA promising new process for the regeneration of solvents with ionic liquid by molecular distillation has been proposed. The main advantage of this process compared with the classic stripping of acids with alkali solution is that the volatile organic acid is recovered with a yield of about 88 % in the form of free acid, not as its salt. Furthermore, improvement on the yield of the stripping can be assumed. The consumption of chemicals in stripping by molecular distillation is reduced.
Spectroscopic and magnetic evidence of coordination properties of bioactive diethyl (pyridin-4-ylmethyl)phosphate ligand with chloride transition-metal ions
Authors: Kalinowska-Lis Urszula , Żurowska Bogumiła , Ochocki Justyn 
Published: June 2011

AbstractA series of five chloride coordination compounds of diethyl (pyridin-4-ylmethyl)phosphate (4-pmOpe) ligand, i.e. [CuCl2(4-pmOpe)2], [NiCl2(4-pmOpe)4], [CoCl2(4-pmOpe)], [ZnCl2(4-pmOpe)2], and [CdCl2(4-pmOpe)2], was prepared and studied. Stoichiometry and stereochemistry of the compounds was confirmed by spectroscopic and magnetic studies as well as by elemental analyses. The 4-pmOpe ligand has a capacity to coordinate to metal ions by means of phosphoryl oxygen and/or nitrogen of pyridine atoms. In Cu(II), Ni(II), and Zn(II) compounds, 4-pmOpe adopts the monodentate coordination mode, bonding metal centers through the pyridine nitrogen atom only. On the contrary, in Co(II) and Cd(II) compounds, 4-pmOpe acts as N,O-bridging ligand forming polynuclear structures. Magnetic studies (1.8–300 K) indicate mononuclear structure of the Co(II) and Ni(II) compounds and suggest existence of a very weak exchange coupling between metal centers in crystal lattice.
Asymmetric single‐strand conformation polymorphism: An accurate and cost‐effective method to amplify and sequence allelic variants
Authors: Rodríguez Flor , Cai Danying , Teng Yuanwen , Spooner David 
Published: June 2011

• Premise of the study: An efficient alternative strategy to conventional cloning was needed to generate high‐quality DNA sequences from a variety of nuclear orthologs for phylogenetic studies. This method would facilitate studies and minimize technical problems typically encountered in cloning methodologies.• Methods: We tested a variety of single‐strand conformation polymorphism (SSCP) protocols including purified and unpurified symmetric and asymmetric PCR, loading buffers, and electrophoresis conditions (buffers, matrix, running time, temperature). Results obtained from direct SSCP band sequencing were compared to those obtained from cloning.• Key results: Our optimized protocol uses asymmetric PCR, with the majority of the samples run in polyacrylamide gel electrophoresis (PAGE). It consistently separated PCR products from 450 to 1200 bp.• Conclusions: Asymmetric PCR single‐strand conformation polymorphism is an efficient alternative technique for isolating allelic variants of highly heterozygous individuals, with its greatest applications in sequencing allopolyploids. It eliminates two common problems encountered in cloning: PCR recombination and heteroduplex fixation. In addition, our protocol greatly lowers costs and time associated with procedures.
Geographic distribution of genetic variation among native and introduced populations of Chinese tallow tree, Triadica sebifera (Euphorbiaceae)
Authors: DeWalt Saara J. , Siemann Evan , Rogers William E. 
Published: June 2011

• Premise of the study: Invasive plants often display genetically determined variation in patterns of growth and resource allocation between native and introduced genotypes, as well as among genotypes within different regions of the introduced range. We examined patterns of genetic variation within and among native and introduced populations of the tetraploid Chinese tallow tree (Triadica sebifera, Euphorbiaceae) to determine whether nonselective evolutionary processes or the introduction history could contribute to previously observed phenotypic differences between native and introduced populations as well as among introduced populations.• Methods: We used six microsatellite markers to study 12 native populations in China, 51 introduced populations in the southeastern USA, and one introduced population in Australia.• Key results: Genetic diversity was greater within and among native populations than introduced populations. Within the southeastern USA, populations in Georgia and South Carolina differed substantially in their genetic composition and had greater genetic diversity than the rest of the southeastern USA. Greater genetic similarity between some populations in the native range and introduced range indicate a common provenance for Georgia and South Carolina populations that could have come from any of several western or southern Chinese populations and a different provenance for other southeastern USA populations and the Australian population, which were most similar to more northeastern Chinese populations.• Conclusions: Differences among introduced populations in potentially adaptive traits (e.g., herbivore tolerance, herbivore resistance, growth rates) may result in part from the introduction history, in particular from differences present among source populations in the native range.
Characterization of rhizosphere fungi from selenium hyperaccumulator and nonhyperaccumulator plants along the eastern Rocky Mountain Front Range
Authors: Wangeline Ami L. , Valdez J. Rodolfo , Lindblom Stormy Dawn , Bowling Keri L. , Reeves F. Brent , Pilon‐Smits Elizabeth A. H. 
Published: June 2011

•Premise of study:Selenium‐hyperaccumulator plants can store over 1% (dry mass) Se in their tissues, despite the toxicity of this element at high concentrations across eukaryotes. These levels of Se can have widespread effects on the plant's ecological partners, including herbivores and pathogens. Still other partners seem to have coevolved Se tolerance. This is the first known study addressing the rhizosphere mycoflora of Se hyperaccumulators and aims to evaluate the rhizospheric fungal diversity and Se tolerance to further the knowledge of how these organisms interact with their host plants and survive in these extreme habitats.•Methods:Rhizosphere fungi were isolated from Se‐hyperaccumulator and nonaccumulator plant species collected from five sites in Colorado and Wyoming; four seleniferous sites and one nonseleniferous site. 259 isolates were identified to genus or species and evaluated for Se tolerance.•Key results:Among the 24 represented genera, 11 comprised 86% of the isolates. The majority of isolates from the seleniferous sites were unaffected by 10 mg·L−1Se, irrespective of host plant (hyperaccumulator vs. nonaccumulator), while rhizosphere fungi from a control, nonseleniferous site were highly sensitive to Se at 10 mg·L−1and as a group were significantly less (α = 0.05) tolerant than the isolates from the seleniferous sites.•Conclusions:Even though Se is a commonly used antifungal agent, these results suggest that rhizosphere fungi from seleniferous habitats have widespread Se tolerance, likely an adaptive advantage in their Se‐rich habitat.
A set of novel microsatellite markers developed for the traditional Tibetan medicinal plant Halenia elliptica (Gentianaceae)
Authors: Zhang Zhi‐Rong , Yang Jing , Sun Yao , Gao Tian‐Gang , Li De‐Zhu , Xue Chun‐Ying 
Published: June 2011

• Premise of the study: Microsatellite primers were developed in the traditional Tibetan medicinal plant Halenia elliptica D. Don to investigate its genetic diversity and population genetic structure.• Methods and Results: Using the Fast Isolation by AFLP of Sequences Containing (FIASCO) repeats protocol, 24 primer sets were identified in two wild populations. Of these primers, 12 displayed polymorphisms and 12 were monomorphic. The number of alleles per locus ranged from 2 to 6, with a mean of 3.9. The expected (HE) and observed (HO) heterozygosities ranged from 0.191 to 0.784 and from 0.417 to 0.917, respectively. All these primers successfully amplified in two close relatives of H. elliptica, Swertia bimaculata (Siebold & Zucc.) Hook. f. & Thomson ex C. B. Clarke and S. tetraptera Maxim.• Conclusions: These markers will facilitate further studies on the population genetics of Halenia elliptica and its allied species.
Ginsenoside Rg1, a Novel Glucocorticoid Receptor Agonist of Plant Origin, Maintains Glucocorticoid Efficacy with Reduced Side Effects
Authors: Du Juan , Cheng Binbin , Zhu Xiaoyan , Ling Changquan 
Published: June 2011

Abstract
Glucocorticoids (GCs) are widely used to treat inflammatory diseases. However, they cause debilitating side effects, which limit the use of these compounds. In the past decade, many researchers have attempted to find so-called dissociated GCs that have separate distinct transactivation and transrepression activities. Anti-inflammation of GCs is a result of glucocorticoid receptor (GR)-mediated transactivation and transrepression in some tissues, similar to their side effects; therefore, the goal to discover a compound that has anti-inflammatory properties, but lacks the negative side effects seen with GCs, has yet to be achieved. In the present study, we introduce a plant-derived compound, ginsenoside Rg1, which possesses GC and estrogen-like activities. In this study, we show that Rg1 downmodulates LPS-induced proinflammatory cytokine release and inhibits NF-κB nuclear translocation and DNA binding activity. The negative effects on NF-κB activation are due to a decrease in IκB phosphorylation and protein stabilization. Furthermore, the inhibitory effect of Rg1 on NF-κB is GR-dependent, as small interfering RNA knockdown of GR abrogated this function. Rg1 also displayed profound inhibitory effects on LPS-induced MAPK activation. Importantly, Rg1 did not impair proliferation or differentiation of mouse osteoblasts. Finally, we show that Rg1 can effectively inhibit acute and chronic inflammation in vivo, but it does not cause hyperglycemia or osteoporosis as seen with dexamethasone. These results suggest that ginsenoside Rg1 may serve as a novel anti-inflammatory agent and may exhibit a potential profile for therapeutic intervention in inflammatory diseases.
Functional Specializations of Intestinal Dendritic Cell and Macrophage Subsets That Control Th17 and Regulatory T Cell Responses Are Dependent on the T Cell/APC Ratio, Source of Mouse Strain, and Regional Localization
Authors: Denning Timothy L. , Norris Brian A. , Medina-Contreras Oscar , Manicassamy Santhakumar , Geem Duke , Madan Rajat , Karp Christopher L. , Pulendran Bali 
Published: June 2011

Abstract
Although several subsets of intestinal APCs have been described, there has been no systematic evaluation of their phenotypes, functions, and regional localization to date. In this article, we used 10-color flow cytometry to define the major APC subsets in the small and large intestine lamina propria. Lamina propria APCs could be subdivided into CD11c+CD11b−, CD11c+CD11b+, and CD11cdullCD11b+ subsets. CD11c+CD11b− cells were largely CD103+F4/80− dendritic cells (DCs), whereas the CD11c+CD11b+ subset comprised CD11c+CD11b+CD103+F4/80− DCs and CD11c+CD11b+CD103−F4/80+ macrophage-like cells. The majority of CD11cdullCD11b+ cells were CD103−F4/80+ macrophages. Although macrophages were more efficient at inducing Foxp3+ regulatory T (Treg) cells than DCs, at higher T cell/APC ratios, all of the DC subsets efficiently induced Foxp3+ Treg cells. In contrast, only CD11c+CD11b+CD103+ DCs efficiently induced Th17 cells. Consistent with this, the regional distribution of CD11c+CD11b+CD103+ DCs correlated with that of Th17 cells, with duodenum &gt; jejunum &gt; ileum &gt; colon. Conversely, CD11c+CD11b−CD103+ DCs, macrophages, and Foxp3+ Treg cells were most abundant in the colon and scarce in the duodenum. Importantly, however, the ability of DC and macrophage subsets to induce Foxp3+ Treg cells versus Th17 cells was strikingly dependent on the source of the mouse strain. Thus, DCs from C57BL/6 mice from Charles River Laboratories (that have segmented filamentous bacteria, which induce robust levels of Th17 cells in situ) were more efficient at inducing Th17 cells and less efficient at inducing Foxp3+ Treg cells than DCs from B6 mice from The Jackson Laboratory. Thus, the functional specializations of APC subsets in the intestine are dependent on the T cell/APC ratio, regional localization, and source of the mouse strain.
Protein Kinase C and NF-κB–Dependent CD4 Downregulation in Macrophages Induced by T Cell-Derived Soluble Factors: Consequences for HIV-1 Infection
Authors: Raposo Rui André Saraiva , Trudgian David C. , Thomas Benjamin , Wilgenburg Bonnie van , Cowley Sally A. , James William 
Published: June 2011

AbstractUpon activation, CD4+ T cells release cytokines, chemokines, and other soluble factors that influence the kinetics of HIV-1 replication in macrophages (Mϕ). In this article, we show that activation of human primary T cells suppresses the early stages of HIV-1 replication in human primary Mϕ by downregulating the main cellular receptor for the virus CD4. The secreted factors responsible for this effect have a molecular mass greater than conventional cytokines, are independent of Th1 or Th2 polarization, and are not IFN-γ, IL-16, RANTES, or macrophage inhibitory factor, as revealed by cytokine array analysis and neutralization assays. CD4 downregulation is entirely posttranslational and involves serine phosphorylation of CD4 and its targeting to an intracellular compartment destined for acidification and degradation. CD4 downregulation is dependent on the activities of both protein kinase C and NF-κB as well as the proteasomes. Using high-resolution liquid chromatography-tandem mass spectrometry analysis in conjugation with label-free protein quantitation software, we found that proteins that promote Mϕ adherence and spreading, such as attractin, fibronectin, and galectin-3–binding protein, were significantly overrepresented in the activated T cell supernatant fractions. These results reveal the existence of previously unreported anti–HIV-1 proteins, released by activated T cells that downregulate CD4 expression, and are of fundamental importance to understand the kinetics of HIV infection in vivo.
Suppression of TLR9 Immunostimulatory Motifs in the Genome of a Gammaherpesvirus
Authors: Pezda Andrea C. , Penn Alex , Barton Gregory M. , Coscoy Laurent 
Published: June 2011

Abstract
Multiple receptors within the innate immune system have evolved to recognize nucleic acids as signatures of viral infection. It is believed that this specificity is essential for viral detection, as viruses often lack other invariant features that can serve as suitable targets for innate receptors. One such innate receptor, TLR9, has been implicated in the detection of many dsDNA viruses. In this study, we investigate the detection of murine gammaherpesvirus 68 (MHV68) by TLR9. We find that the genomic DNA of the murine CMV, a very potent inducer of innate responses. Genome-wide analysis of the number of stimulatory versus nonstimulatory CpG motifs present in the genome of each virus reveals that the MHV68 genome contains only a fraction of the number of immunostimulatory motifs present in murine CMV. Notably, MHV68 appears to have selectively suppressed the number of stimulatory motifs through cytosine to thymine conversion. These data suggest that certain viruses may have evolved and modified their genomic content to avoid recognition by nucleic acid-sensing receptors of the innate immune system.