bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of cation exchange capacity from soil index properties
Authors: Yukselen Y. , Kaya A. 
Published: December 2006

AbstractIn many areas of geotechnical engineering it is necessary to have an estimate of the cation exchange capacity (CEC) of a soil in order to allow preliminary design estimates. Standard methods of CEC determination are time-consuming and involve several steps (e.g. displacement of the saturating cation requires several washings with alcohol). Therefore, a rapid method of CEC estimation would be very useful. During preliminary site investigations, the soil engineering parameters can be estimated from the considerable number of correlations available in the literature. In this study, relationships between CEC and various other soil engineering properties have been investigated, resulting in a quick method for estimating CEC.Simple correlations were developed between CEC and specific surface area (SSA), soil organic matter (OM), clay fraction (CF), activity (A), Atterberg limits (liquid (LL), plastic (PL), and shrinkage (SL)), and modified free swell index (MFSI) of the soils. Strong correlations are observed between the CEC values and those for ethylene glycol monoethyl ether (EGME) uptake and methylene blue (MB) titration. However, no significant correlation was found between CEC and N2_SSA. No unique relationship was seen between CEC and CF (r2<0.5). No relationship was observed between CEC and OM in this study. The best correlation coefficient between the CEC and Atterberg limits exists between CEC and LL (r2= 0.61). No significant relationship was seen between CEC and PL or SL. The correlation coefficient between CEC and MFSI was 0.65. Multiple linear regression analyses were developed to investigate the contributions of different soil parameters to CEC. These analyses show that EGME_SSA, in combination with LL, accounted for 91% of the variation in CEC. Correlations between CEC and EGME_SSA, MB_SSA and LL appear to be sufficiently good to enable an indication of CEC to be estimated from these parameters.
Stratigraphic variations in mudstone mineral assemblages from a submarine fan-complex: Karoo Basin, South Africa
Authors: Andersson P. O. D. , Worden R. H. 
Published: December 2006

AbstractDespite the high-grade diagenesis experienced by the Skoorsteenberg Formation mudstones, Tanqua Karoo basin, South Africa, geochemical data have been interpreted to reveal primary mineralogy and so help understand provenance evolution. The geochemical signatures show systematic variations related to stratigraphy. The main changes in mudstones from the lower to the upper part of the section include: (1) an increase in the feldspar content of the primary sediment and a decrease in the content of Al-rich clay (probably dioctahedral smectite); (2) a decrease in the degree of chemical weathering of the sediment, representing a change to a dryer and/or cooler climate; (3) an increase in TiO2/Al2O3 representing increasing mafic sources; (4) an increase in CaO/(K2O+CaO) also possibly representing increasing mafic sources. Mass flux and differential diagenesis are unlikely to be responsible for the depth-related changes since the rocks have undergone the same degree of high-grade diagenesis and the mudstones are interrupted by other lithologies, so disturbing any sort of diffusion gradient. These variations could plausibly be the result of one or more of differential weathering, evolving provenance characteristics or variable hydrodynamic fractionation of the sediment. The ratio of Zr/Y, a possible indicator of hydrodynamic fractionation, increases only slightly and irregularly up-section. There is no relationship between the silica content, representative of the quartz-silt content of the sediment, and TiO2/Al2O3 showing that the amount of quartz, and so the degree of hydrodynamic fractionation, has not controlled mudstone geochemistry. The stratigraphic increase in feldspar content, the decrease in Al-rich clay content and increase of both TiO2/Al2O3 and CaO/(K2O+CaO) must be due to a combination of marginally evolving provenance characteristics (more mafic and felsic rocks exposed to weathering with time) and changes in the degree of rock weathering (less chemical weathering with time).
The effects of electrolyte concentration, ion species and pH on the zeta potential and electrokinetic charge density of montmorillonite
Authors: Saka E. E. , Güler C. 
Published: December 2006

AbstractIn this study, the influence of pH, electrolyte concentration and type of ionic species (such as LiCl, NaCl, KCl, RbCl, CsCl, CaCl2, AlCl3) on the electrokinetic properties (zeta potential and electrokinetic charge density) of montmorillonite has been quantified. The zeta potential of montmorillonite particles did not change significantly with change in pH. The valencies of the ions have proven to have a great influence on the electrokinetic behaviour of the suspension. There is a gradual decrease in the zeta potential (from —24 mV to —12 mV) with increase in monovalent electrolyte concentration (from 10-4 M to 10-1 M). At any monovalent electrolyte concentration, the magnitude of the zeta potential increased with the electrolytes in the order Li+ > Na+ > K+ > Rb+ > Cs+. The zeta potential of the montmorillonite minerals in CaCl2 solutions illustrated the same behaviour as the monovalent cations. Less negative values were obtained for the CaCl2 electrolyte (∼–10 mV) due to the greater valence of the ions. A sign reversal was observed at an AlCl3 concentration of 5 x 10-4 M, and, at greater concentrations, zeta potential values had a positive sign (∼20 mV).The electrokinetic charge density of montmorillonite showed similar trends of variation in mono and divalent electrolyte solutions. Up to concentrations of ∼10-3 M, it remained practically constant at ∼0.5 x 10-3Cm-2, while for greater electrolyte concentrations the negative charge produced more negative values (–16 x 10-3Cm-2). The electrokinetic charge density of montmorillonite particles was constant at low AlCl3 concentrations, but at certain concentrations it increased rapidly and changed sign to positive.
Stimulation of P2 receptors causes release of IL-1β–loaded microvesicles from human dendritic cells
Authors: Pizzirani Cinzia , Ferrari Davide , Chiozzi Paola , Adinolfi Elena , Sandonà Dorianna , Savaglio Erika , Di Virgilio Francesco 
Published: December 2006

AbstractDendritic cells (DCs) are professional antigen-presenting cells that initiate the immune response by activating T lymphocytes. DCs express plasma membrane receptors for extracellular nucleotides named P2 receptors (P2Rs). Stimulation of P2Rs in these cells is known to cause chemotaxis, cytokine release, and cell death and to modulate LPS-dependent differentiation. Here we show that stimulation of the P2X7 receptor subtype (P2X7R) causes fast microvesicle shedding from DC plasma membrane. Vesicle release occurs from both immature and mature DCs; however, only vesicles from mature DCs, due to their previous exposure to LPS, contain IL-1β. Microvesicles, whether from immature or mature DCs, also contain caspase-1 and -3 and cathepsin D. They also express the P2X7R in addition to other P2Rs and known markers of immune cells such as major histocompatibility complex II (MHC II) and CD39. Activation of the P2X7R by extracellular ATP causes IL-1β release from the vesicle lumen. Previous studies demonstrated that high extracellular K+ inhibits IL-1β processing and release; here we show that high ionic strength reduces microvesicle shedding when compared with a low ionic strength medium but strongly increases microvesicle IL-1β loading.
Abcb7, the gene responsible for X-linked sideroblastic anemia with ataxia, is essential for hematopoiesis
Authors: Pondarre Corinne , Campagna Dean R. , Antiochos Brendan , Sikorski Lindsay , Mulhern Howard , Fleming Mark D. 
Published: December 2006

AbstractX-linked sideroblastic anemia with ataxia (XLSA/A) is a rare syndromic form of inherited sideroblastic anemia associated with spinocerebellar ataxia, and is due to mutations in the mitochondrial ATP-binding cassette transporter Abcb7. Here, we show that Abcb7 is essential for hematopoiesis and formally demonstrate that XLSA/A is due to partial loss of function mutations in Abcb7 that directly or indirectly inhibit heme biosynthesis.
Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins
Authors: Macaulay Iain C. , Tijssen Marloes R. , Thijssen-Timmer Daphne C. , Gusnanto Arief , Steward Michael , Burns Philippa , Langford Cordelia F. , Ellis Peter D. , Dudbridge Frank , Zwaginga Jaap-Jan , Watkins Nicholas A. , van der Schoot C. Ellen , Ouwehand Willem H. 
Published: December 2006

AbstractTo identify previously unknown platelet receptors we compared the transcriptomes of in vitro differentiated megakaryocytes (MKs) and erythroblasts (EBs). RNA was obtained from purified, biologically paired MK and EB cultures and compared using cDNA microarrays. Bioinformatical analysis of MK–up-regulated genes identified 151 transcripts encoding transmembrane domain-containing proteins. Although many of these were known platelet genes, a number of previously unidentified or poorly characterized transcripts were also detected. Many of these transcripts, including G6b, G6f, LRRC32, LAT2, and the G protein–coupled receptor SUCNR1, encode proteins with structural features or functions that suggest they may be involved in the modulation of platelet function. Immunoblotting on platelets confirmed the presence of the encoded proteins, and flow cytometric analysis confirmed the expression of G6b, G6f, and LRRC32 on the surface of platelets. Through comparative analysis of expression in platelets and other blood cells we demonstrated that G6b, G6f, and LRRC32 are restricted to the platelet lineage, whereas LAT2 and SUCNR1 were also detected in other blood cells. The identification of the succinate receptor SUCNR1 in platelets is of particular interest, because physiologically relevant concentrations of succinate were shown to potentiate the effect of low doses of a variety of platelet agonists.
Pathogenic proline mutation in the linker between spectrin repeats: disease caused by spectrin unfolding
Authors: Johnson Colin P. , Gaetani Massimiliano , Ortiz Vanessa , Bhasin Nishant , Harper Sandy , Gallagher Patrick G. , Speicher David W. , Discher Dennis E. 
Published: December 2006

AbstractPathogenic mutations in α and β spectrin result in a variety of syndromes, including hereditary elliptocytosis (HE), hereditary pyropoikilocytosis (HPP), and hereditary spherocytosis (HS). Although some mutations clearly lie at sites of interaction, such as the sites of spectrin α-βtetramer formation, a surprising number of HE-causing mutations have been identified within linker regions between distal spectrin repeats. Here we apply solution structural and single molecule methods to the folding and stability of recombinant proteins consisting of the first 5 spectrin repeats of α-spectrin, comparing normal spectrin with a pathogenic linker mutation, Q471P, between repeats R4 and R5. Results show that the linker mutation destabilizes a significant fraction of the 5-repeat construct at 37°C, whereas the WT remains fully folded well above body temperature. In WT protein, helical linkers propagate stability from one repeat to the next, but the mutation disrupts the stabilizing influence of adjacent repeats. The results suggest a molecular mechanism for the high frequency of disease caused by proline mutations in spectrin linkers.
Differential effects of IL-21 and IL-15 on perforin expression, lysosomal degranulation, and proliferation in CD8 T cells of patients with human immunodeficiency virus-1 (HIV)
Authors: White Lesley , Krishnan Subramaniam , Strbo Natasa , Liu Huanliang , Kolber Michael A. , Lichtenheld Mathias G. , Pahwa Rajendra N. , Pahwa Savita 
Published: December 2006

AbstractAn urgent need exists to devise strategies to augment antiviral immune responses in patients with HIV who are virologically well controlled and immunologically stable on highly active antiretroviral therapy (HAART). The objective of this study was to compare the immunomodulatory effects of the cytokines interleukin (IL)–21 with IL-15 on CD8 T cells in patients with HIV RNA of less than 50 copies/mL and CD4 counts greater than 200 cells/mm.3 Patient CD8 T cells displayed skewed maturation and decreased perforin expression compared with healthy controls. Culture of freshly isolated patient peripheral-blood mononuclear cells (PBMCs) for 5 hours to 5 days with IL-21 resulted in up-regulation of perforin in CD8 T cells, including memory and effector subsets and virus-specific T cells. IL-21 did not induce T-cell activation or proliferation, nor did it augment T-cell receptor (TCR)–induced degranulation. Treatment of patient PBMCs with IL-15 resulted in induction of perforin in association with lymphocyte proliferation and augmentation of TCR-induced degranulation. Patient CD8 T cells were more responsive to cytokine effects than the cells of healthy volunteers. We conclude that CD8 T cells of patients with HIV can be modulated by IL-21 to increase perforin expression without undergoing overt cellular activation. IL-21 could potentially be useful for its perforin-enhancing properties in anti-HIV immunotherapy.
K-RasG12D expression induces hyperproliferation and aberrant signaling in primary hematopoietic stem/progenitor cells
Authors: Van Meter Margaret E. M. , Díaz-Flores Ernesto , Archard Joehleen A. , Passegué Emmanuelle , Irish Jonathan M. , Kotecha Nikesh , Nolan Garry P. , Shannon Kevin , Braun Benjamin S. 
Published: December 2006

AbstractDefining how cancer-associated mutations perturb signaling networks in stem/progenitor populations that are integral to tumor formation and maintenance is a fundamental problem with biologic and clinical implications. Point mutations in RAS genes contribute to many cancers, including myeloid malignancies. We investigated the effects of an oncogenic KrasG12D allele on phosphorylated signaling molecules in primary c-kit+ lin−/low hematopoietic stem/progenitor cells. Comparison of wild-type and KrasG12D c-kit+ lin−/low cells shows that K-RasG12D expression causes hyperproliferation in vivo and results in abnormal levels of phosphorylated STAT5, ERK, and S6 under basal and stimulated conditions. Whereas KrasG12D cells demonstrate hyperactive signaling after exposure to granulocyte-macrophage colony-stimulating factor, we unexpectedly observe a paradoxical attenuation of ERK and S6 phosphorylation in response to stem cell factor. These studies provide direct biochemical evidence that cancer stem/progenitor cells remodel signaling networks in response to oncogenic stress and demonstrate that multi-parameter flow cytometry can be used to monitor the effects of targeted therapeutics in vivo. This strategy has broad implications for defining the architecture of signaling networks in primary cancer cells and for implementing stem cell–targeted interventions.
Linkage disequilibrium of evolutionarily conserved regions in the human genome
Authors: Kato Mamoru , Sekine Akihiro , Ohnishi Yozo , Johnson Todd A , Tanaka Toshihiro , Nakamura Yusuke , Tsunoda Tatsuhiko 
Published: December 2006

Abstract

Background
The strong linkage disequilibrium (LD) recently found in genic or exonic regions of the human genome demonstrated that LD can be increased by evolutionary mechanisms that select for functionally important loci. This suggests that LD might be stronger in regions conserved among species than in non-conserved regions, since regions exposed to natural selection tend to be conserved. To assess this hypothesis, we used genome-wide polymorphism data from the HapMap project and investigated LD within DNA sequences conserved between the human and mouse genomes.

Results
Unexpectedly, we observed that LD was significantly weaker in conserved regions than in non-conserved regions. To investigate why, we examined sequence features that may distort the relationship between LD and conserved regions. We found that interspersed repeats, and not other sequence features, were associated with the weak LD tendency in conserved regions. To appropriately understand the relationship between LD and conserved regions, we removed the effect of repetitive elements and found that the high degree of sequence conservation was strongly associated with strong LD in coding regions but not with that in non-coding regions.

Conclusion
Our work demonstrates that the degree of sequence conservation does not simply increase LD as predicted by the hypothesis. Rather, it implies that purifying selection changes the polymorphic patterns of coding sequences but has little influence on the patterns of functional units such as regulatory elements present in non-coding regions, since the former are generally restricted by the constraint of maintaining a functional protein product across multiple exons while the latter may exist more as individually isolated units.
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
Authors: Campbell Matthew A , Haas Brian J , Hamilton John P , Mount Stephen M , Buell C Robin 
Published: December 2006

Abstract

Background
Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST) libraries. We employed the Program to Assemble Spliced Alignments (PASA) to identify and analyze alternatively spliced isoforms in both species.

Results
A comprehensive analysis of alternative splicing was performed in rice that started with >1.1 million publicly available spliced ESTs and over 30,000 full length cDNAs in conjunction with the newly enhanced PASA software. A parallel analysis was performed with Arabidopsis to compare and ascertain potential differences between monocots and dicots. Alternative splicing is a widespread phenomenon (observed in greater than 30% of the loci with transcript support) and we have described nine alternative splicing variations. While alternative splicing has the potential to create many RNA isoforms from a single locus, the majority of loci generate only two or three isoforms and transcript support indicates that these isoforms are generally not rare events. For the alternate donor (AD) and acceptor (AA) classes, the distance between the splice sites for the majority of events was found to be less than 50 basepairs (bp). In both species, the most frequent distance between AA is 3 bp, consistent with reports in mammalian systems. Conversely, the most frequent distance between AD is 4 bp in both plant species, as previously observed in mouse. Most alternative splicing variations are localized to the protein coding sequence and are predicted to significantly alter the coding sequence.

Conclusion
Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features. Interestingly, alternative splicing may play a role beyond creating novel combinations of transcripts that expand the proteome. Many isoforms will presumably have negative consequences for protein structure and function, suggesting that their biological role involves post-transcriptional regulation of gene expression.
Detection of transcriptional difference of porcine imprinted genes using different microarray platforms
Authors: Tsai Shengdar , Mir Bashir , Martin Amy C , Estrada Jose L , Bischoff Steve R , Hsieh Wen-ping , Cassady Joseph P , Freking Bradley A , Nonneman Dan J , Rohrer Gary A , Piedrahita Jorge A 
Published: December 2006

Abstract

Background
Presently, multiple options exist for conducting gene expression profiling studies in swine. In order to determine the performance of some of the existing microarrays, Affymetrix Porcine, Affymetrix Human U133+2.0, and the U.S. Pig Genome Coordination Program spotted glass oligonucleotide microarrays were compared for their reproducibility, coverage, platform independent and dependent sensitivity using fibroblast cell lines derived from control and parthenogenic porcine embryos.

Results
Array group correlations between technical replicates demonstrated comparable reproducibility in both Affymetrix arrays. Glass oligonucleotide arrays showed greater variability and, in addition, approximately 10% of probes had to be discarded due to slide printing defects. Probe level analysis of Affymetrix Human arrays revealed significant variability within probe sets due to the effects of cross-species hybridization. Affymetrix Porcine arrays identified the greatest number of differentially expressed genes amongst probes common to all arrays, a measure of platform sensitivity. Affymetrix Porcine arrays also identified the greatest number of differentially expressed known imprinted genes using all probes on each array, an ad hoc measure of realistic performance for this particular experiment.

Conclusion
We conclude that of the platforms currently available and tested, the Affymetrix Porcine array is the most sensitive and reproducible microarray for swine genomic studies.
Reduced repair of 8-hydroxyguanine in the human breast cancer cell line, HCC1937
Authors: Nyaga Simon G , Lohani Althaf , Jaruga Pawel , Trzeciak Andrzej R , Dizdaroglu Miral , Evans Michele K 
Published: December 2006

Abstract

Background
Breast cancer is the second leading cause of cancer deaths in women in the United States. Although the causes of this disease are incompletely understood, oxidative DNA damage is presumed to play a critical role in breast carcinogenesis. A common oxidatively induced DNA lesion is 8-hydroxyguanine (8-OH-Gua), which has been implicated in carcinogenesis. The aim of this study was to investigate the ability of HCC1937 and MCF-7 breast cancer cell lines to repair 8-OH-Gua relative to a nonmalignant human mammary epithelial cell line, AG11134.

Methods
We used oligonucleotide incision assay to analyze the ability of the two breast cancer cell lines to incise 8-OH-Gua relative to the control cell line. Liquid chromatography/mass spectrometry (LC/MS) was used to measure the levels of 8-OH-Gua as its nucleoside, 8-OH-dG in the cell lines after exposure to H2O2 followed by 30 min repair period. Protein expression levels were determined by Western blot analysis, while the hOGG1 mRNA levels were analyzed by RT-PCR. Complementation of hOGG1 activity in HCC1937 cells was assessed by addition of the purified protein in the incision assay, and in vivo by transfection of pFlagCMV-4-hOGG1. Clonogenic survival assay was used to determine sensitivity after H2O2-mediated oxidative stress.

Results
We show that the HCC1937 breast cancer cells have diminished ability to incise 8-OH-Gua and they accumulate higher levels of 8-OH-dG in the nuclear genome after H2O2 treatment despite a 30 min repair period when compared to the nonmalignant mammary cells. The defective incision of 8-OH-Gua was consistent with expression of undetectable amounts of hOGG1 in HCC1937 cells. The reduced incision activity was significantly stimulated by addition of purified hOGG1. Furthermore, transfection of pFlagCMV-4-hOGG1 in HCC1937 cells resulted in enhanced incision of 8-OH-Gua. HCC1937 cells are more sensitive to high levels of H2O2 and have up-regulated SOD1 and SOD2.

Conclusion
This study provides evidence for inefficient repair of 8-OH-Gua in HCC1937 breast cancer cell line and directly implicates hOGG1 in this defect.