bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of glucocorticoid receptor phosphorylation in Mcl-1 and NOXA gene expression
Authors: Lynch James T , Rajendran Ramkumar , Xenaki Georgia , Berrou Ilhem , Demonacos Constantinos , Krstic-Demonacos Marija 
Published: February 2010

Abstract

Background
The cyclin-dependent kinase (CDK) and mitogen-activated protein kinase (MAPK) mediated phosphorylation of glucocorticoid receptor (GR) exerts opposite effects on GR transcriptional activity and affects other posttranslational modifications within this protein. The major phosphorylation site of human GR targeted by MAPK family is the serine 226 and multiple kinase complexes phosphorylate receptor at the serine 211 residue. We hypothesize that GR posttranslational modifications are involved in the determination of the cellular fate in human lymphoblastic leukemia cells. We investigated whether UV signalling through alternative GR phosphorylation determined the cell type specificity of glucocorticoids (GCs) mediated apoptosis.

Results
We have identified putative Glucocorticoid Response Elements (GREs) within the promoter regulatory regions of the Bcl-2 family members NOXA and Mcl-1 indicating that they are direct GR transcriptional targets. These genes were differentially regulated in CEM-C7-14, CEM-C1-15 and A549 cells by glucocorticoids and JNK pathway. In addition, our results revealed that the S211 phosphorylation was dominant in CEM-C7-14, whereas the opposite was the case in CEM-C1-15 where prevalence of S226 GR phosphorylation was observed. Furthermore, multiple GR isoforms with cell line specific patterns were identified in CEM-C7-14 cells compared to CEM-C1-15 and A549 cell lines with the same antibodies.

Conclusions
GR phosphorylation status kinetics, and site specificity as well as isoform variability differ in CEM-C7-14, CEM-C1-15, and A549 cells. The positive or negative response to GCs induced apoptosis in these cell lines is a consequence of the variable equilibrium of NOXA and Mcl-1 gene expression potentially mediated by alternatively phosphorylated GR, as well as the balance of MAPK/CDK pathways controlling GR phosphorylation pattern. Our results provide molecular base and valuable knowledge for improving the GC based therapies of leukaemia.
HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays
Authors: Vandenbroucke Ina , Van Marck Herwig , Mostmans Wendy , Van Eygen Veerle , Rondelez Evelien , Thys Kim , Van Baelen Kurt , Fransen Katrien , Vaira Dolores , Kabeya Kabamba , De Wit Stephane , Florence Eric , Moutschen Michel , Vandekerckhove Linos , Verhofstede Chris , Stuyver Lieven J 
Published: February 2010

AbstractBackgroundHIV-1 infected patients for whom standard gp160 phenotypic tropism testing failed are currently excluded from co-receptor antagonist treatment. To provide patients with maximal treatment options, massively parallel sequencing of the envelope V3 domain, in combination with tropism prediction tools, was evaluated as an alternative tropism determination strategy. Plasma samples from twelve HIV-1 infected individuals with failing phenotyping results were available. The samples were submitted to massive parallel sequencing and to confirmatory recombinant phenotyping using a fraction of the gp120 domain.ResultsA cut-off for sequence reads interpretation of 5 to10 times the sequencing error rate (0.2%) was implemented. On average, each sample contained 7 different V3 haplotypes. V3 haplotypes were submitted to tropism prediction algorithms, and 4/14 samples returned with presence of a dual/mixed (D/M) tropic virus, respectively at 3%, 10%, 11%, and 95% of the viral quasispecies. V3 tropism prediction was confirmed by gp120 phenotyping, except for two out of 4 D/M predicted viruses (with 3 and 95%) which were phenotypically R5-tropic. In the first case, the result was discordant due to the limit of detection for the phenotyping technology, while in the latter case the prediction algorithms were not computing the viral tropism correctly.ConclusionsAlthough only demonstrated on a limited set of samples, the potential of the combined use of "deep sequencing + prediction algorithms" in cases where routine gp160 phenotype testing cannot be employed was illustrated. While good concordance was observed between gp120 phenotyping and prediction of R5-tropic virus, the results suggest that accurate prediction of X4-tropic virus would require further algorithm development.
Kinematic aspects of trunk motion and gender effect in normal adults
Authors: Chung ChinYoub , Park MoonSeok , Lee SangHyeong , Kong SeJin , Lee KyoungMin 
Published: February 2010

Abstract

Background
The purpose of this study was to analyze kinematic trunk motion data in normal adults and to investigate gender effect.

Methods
Kinematic trunk motion data were obtained for 20 healthy subjects (11 men and 9 women; age from 21 to 40 years) during walking a 9 m long lane at a self selected speed, namely, motions in the sagittal (tilt), coronal (obliquity), and transverse (rotation) planes, which were all expressed as motions in global (relative to the ground) and those in pelvic reference frame (relative to pelvis), i.e., tilt (G), obliquity (G), rotation (G), tilt (P), obliquity (P), rotation (P).

Results
Range of tilt (G), obliquity (G) and rotation (G) showed smaller motion than that of tilt (P), obliquity (P) and rotation (P), respectively. When genders were compared, female trunks showed a 5 degree more extended posture during gait than male trunks (p = 0.002), which appeared to be caused by different lumbar lordosis. Ranges of coronal and transverse plane motion appeared to be correlated. In gait cycle, the trunk motion appeared to counterbalance the lower extremity during swing phase in sagittal plane, and to reduce the angular velocity toward the contralateral side immediate before the contralateral heel strike in the coronal plane.

Conclusions
Men and women showed different lumbar lordosis during normal gait, which might be partly responsible for the different prevalence of lumbar diseases between genders. However, this needs further investigation.
Functional consequences of DECTIN-1early stop codon polymorphism Y238X in rheumatoid arthritis
Authors: Plantinga Theo S , Fransen Jaap , Takahashi Nozomi , Stienstra Rinke , van Riel Piet L , van den Berg Wim B , Netea Mihai G , Joosten Leo AB 
Published: February 2010

Abstract
Introduction
Dectin-1, a pattern recognition receptor expressed by the innate immune system, is known to be a major receptor inducing Th17-type adaptive immune responses that have been demonstrated to mediate autoimmunity. In this study, dectin-1 mRNA and protein expression, as well as the recently characterized DECTIN-1 Y238X early stop codon polymorphism, were studied in relation to rheumatoid arthritis (RA) susceptibility and severity.

Methods
Dectin-1 mRNA expression was measured in synovial tissue specimens of RA, osteoarthritis (OA), and nonrheumatic patients. Dectin-1 protein expression and localization were assessed in RA synovial tissue specimens. Macrophages from individuals with different DECTIN-1 genotypes were examined for differences in cytokine responses on dectin-1 stimulation. Furthermore, clinical parameters of inflammation and bone destruction of 262 RA patients were correlated with the presence of the DECTIN-1 Y238X polymorphism.

Results
Evaluation of dectin-1 mRNA expression in synovial tissue biopsies revealed an increased expression in RA specimens, compared with biopsies from OA and nonrheumatic patients. Accordingly, dectin-1 protein expression in RA synovial tissue biopsies was moderate to high, especially on macrophage-like cells. Cytokine production capacity of macrophages bearing the DECTIN-1 Y238X polymorphism was demonstrated to be impaired on dectin-1 stimulation. However, the presence of the DECTIN-1 Y238X polymorphism was not associated with RA susceptibility or disease severity.

Conclusions
Although expression of dectin-1 was high in synovial tissue of RA patients, and reduced cytokine production was observed in macrophages of individuals bearing the DECTIN-1 Y238X polymorphism, loss of one functional allele of DECTIN-1 is not associated with either susceptibility to or severity of RA.
A fuzzy gene expression-based computational approach improves breast cancer prognostication
Authors: Haibe-Kains Benjamin , Desmedt Christine , Rothé Françoise , Piccart Martine , Sotiriou Christos , Bontempi Gianluca 
Published: February 2010

AbstractEarly gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative breast cancers, few are informative for ER negative/HER2 negative and HER2 positive subtypes. Here we present Gene Expression Prognostic Index Using Subtypes (GENIUS), a fuzzy approach for prognostication that takes into account the molecular heterogeneity of breast cancer. In systematic evaluations, GENIUS significantly outperformed current gene signatures and clinical indices in the global population of patients.
Genomic features defining exonic variants that modulate splicing
Authors: Woolfe Adam , Mullikin James C , Elnitski Laura 
Published: February 2010

Abstract
Background
Single point mutations at both synonymous and non-synonymous positions within exons can have severe effects on gene function through disruption of splicing. Predicting these mutations in silico purely from the genomic sequence is difficult due to an incomplete understanding of the multiple factors that may be responsible. In addition, little is known about which computational prediction approaches, such as those involving exonic splicing enhancers and exonic splicing silencers, are most informative.

Results
We assessed the features of single-nucleotide genomic variants verified to cause exon skipping and compared them to a large set of coding SNPs common in the human population, which are likely to have no effect on splicing. Our findings implicate a number of features important for their ability to discriminate splice-affecting variants, including the naturally occurring density of exonic splicing enhancers and exonic splicing silencers of the exon and intronic environment, extensive changes in the number of predicted exonic splicing enhancers and exonic splicing silencers, proximity to the splice junctions and evolutionary constraint of the region surrounding the variant. By extending this approach to additional datasets, we also identified relevant features of variants that cause increased exon inclusion and ectopic splice site activation.

Conclusions
We identified a number of features that have statistically significant representation among exonic variants that modulate splicing. These analyses highlight putative mechanisms responsible for splicing outcome and emphasize the role of features important for exon definition. We developed a web-tool, Skippy, to score coding variants for these relevant splice-modulating features.
New insights into tooth wear based on in vitro studies
Authors: Richards L C , Kaidonis J A , Townsend G C 
Published: February 2010

in vitro experimental systems for the study of tooth wear have the potential to overcome the long time frames and ethical complexities involved in undertaking clinical studies. The aim of this article is to review in vitro studies undertaken by the authors and highlight areas in which significant progress has been made. Investigations of enamel, dentine, and restorative material wear and potential wear-prevention strategies were conducted using a purpose-built wear simulation machine with loads between 32 and 160 N and with specimens lubricated by solutions at pH = 6-7 (simulating a serous oral environment), pH = 3 (resembling an acidic diet), pH = 1.2 (resembling regurgitated acid), or with pooled natural saliva (pH = 7). These studies have demonstrated a linear relationship between load and the rate of dentine wear and very low wear rates for enamel except at the highest loads (when enamel and dentine wear at similar rates) and at the lowest pHs (when both enamel and dentine wear rapidly). Comparisons of wear rates for enamel and common restorative materials have shown that at low pH, the enamel tends to wear more rapidly than any of the materials considered: resin composites are more resistant to acid and high loads than glass-ionomer cements (GICs); resin-modified GICs have intermediate properties; and, most modern dental porcelains wear at about the same rate as opposing enamel. Recent studies of preventive strategies have provided evidence of the wear-reducing potential of both lubricants and remineralizing agents. Considered together, these studies have given a clearer understanding of the factors that influence the wear of enamel, dentine, and restorations under various conditions.
Effect of Phase Separation on Thermal Aging Behavior of Styrene–Butadiene Rubber Vulcanizates Using Liquid Polyisoprene as Plasticizer
Authors: Nakazono Takeo , Ozaki Anri , Matsumoto Akikazu 
Published: February 2010

Abstract
Styrene–butadiene rubber (SBR) vulcanizates were prepared using liquid polyisoprene (PI) and hydrogenated polyisoprene (HPI) as the plasticizers, and their structure and mechanical properties were investigated. The effect of the phase-separated structures of the SBR and the liquid polymers on the mechanical properties of the SBR vulcanizates was investigated. The constant physical properties were observed for the SBR vulcanizates during the thermal aging process when SBR and the plasticizer were miscible with each other in the vulcanizates.
In Vivo Resonance Raman Detection of Ferrous Cytochrome c from Mitochondria of Single Living Yeast Cells
Authors: Onogi Chikao , Hamaguchi Hiro-o 
Published: February 2010

Abstract
Raman spectra of mitochondria in living budding yeast cells (zygote of Saccharomyces cerevisiae and Saccharomyces bayanus) have been recorded with 532 nm excitation. Strong and sharp Raman bands are observed at 1584, 1315, 1129, 749, and 601 cm−1, in addition to known phospholipid bands. These Raman bands are not observed in the corresponding Raman spectrum of mitochondria obtained with 632.8 nm excitation. Their peak positions and relative intensities agree excellently with the reported resonance-enhanced Raman bands of ferrous cytochrome c, which has a Q-band absorption at 520 nm. We have thus succeeded in detecting ferrous cytochrome c, one of the key intermediates in the electron-transport chain in mitochondria, in vivo without any pretreatment. In vivo resonance Raman detection of ferrous cytochrome c opens up new possibilities for real-time and quantitative tracing of respiration dynamics in mitochondria in a single living cell.
Distribution of Fluorescent Dyes Dissolved in Ternary Mixed Solvent in a Microchannel under Laminar Flow Conditions
Authors: Murakami Mari , Jinno Naoya , Hashimoto Masahiko , Tsukagoshi Kazuhiko 
Published: February 2010

Abstract
We observed chromatographic separation in an open capillary tube with a water–hydrophilic–hydrophobic organic mixture carrier solution. The separation is thought to be based on the tube radial distrubution of aqueous and organic carrier solvents in the capillary tube. In this study, in order to obtain information concerning the solvent distribution, we delivered a carrier solution containing fluorescent dyes into a microchannel (100 µm in width × 40 µm in depth) and monitored the tube radial distribution of the dyes using a fluorescence microscope. When an organic solvent-rich carrier solution (water–acetonitrile–ethyl acetate; 3:8:4 volume ratio) containing perylene and Eosin Y was fed into the channel, perylene and Eosin Y were distributed around the center and near the inner wall of the microchannel, respectively. This observation consists with the specific solvent distribution proposed for the chromatography system.
Secondary Sex Ratio in Multiple Births
Authors: Fellman Johan , Eriksson Aldur W. 
Published: February 2010

AbstractAttempts have been made to identify factors influencing the sex ratio at birth (number of males per 100 females). Statistical analyses have shown that comparisons between sex ratios demand large data sets. The secondary sex ratio has been believed to vary inversely with the frequency of prenatal losses. This hypothesis suggests that the ratio is highest among singletons, medium among twins and lowest among triplets. Birth data in Sweden for the period 1869–2004 showed that among live births the secondary sex ratio was on average 105.9 among singletons, 103.2 among twins and 99.1 among triplets. The secondary sex ratio among stillbirths for both singletons and twins started at a high level, around 130, in the 1860s, but approached live birth values in the 1990s. This trend is associated with the decrease and convergence of stillbirth rates among males and females. For detailed studies, we considered data for Sweden in 1869–1878 and in 1901–1967. Marital status or place of residence (urban or rural) had no marked influence on the secondary sex ratio among twins. For triplets, the sex ratio showed large random fluctuations and was on average low. During the period 1901–1967, 20 quadruplet, two quintuplet and one sextuplet set were registered. The sex ratio was low, around 92.0.
A Twin-Singleton Comparison of Developmental Trajectories of Externalizing and Internalizing Problems in 6- to 12-Year-Old Children
Authors: Robbers Sylvana C. C. , Bartels Meike , van Oort Floor V. A. , van Beijsterveldt C. E. M. (Toos) , van der Ende Jan , Verhulst Frank C. , Boomsma Dorret I. , Huizink Anja C. 
Published: February 2010

AbstractResearch on twin-singleton differences in externalizing and internalizing problems in childhood is largely cross-sectional and yields contrasting results. The goal of this study was to compare developmental trajectories of externalizing and internalizing problems in 6- to 12-year-old twins and singletons. Child Behavior Checklist (CBCL) maternal reports of externalizing and internalizing problems were obtained for a sample of 9651 twins from the Netherlands Twin Register and for a representative general population sample of 1351 singletons. Latent growth modeling was applied to estimate growth curves for twins and singletons. Twin-singleton differences in the intercepts and slopes of the growth curves were examined. The developmental trajectories of externalizing problems showed a linear decrease over time, and were not significantly different for twins and singletons. Internalizing problems seem to develop similarly for twins and singletons up to age 9. After this age twins' internalizing symptoms start to decrease in comparison to those of singletons, resulting in less internalizing problems than singletons by the age of 12 years. Our findings confirm the generalizability of twin studies to singleton populations with regard to externalizing problems in middle and late childhood. The generalizability of studies on internalizing problems in early adolescence in twin samples should be addressed with care. Twinship may be a protective factor in the development of internalizing problems during early adolescence.
Effect of Variations in Practice of ASTM D7522 Standard Pull-Off Test for FRP-Concrete Interfaces
Authors: Eveslage Troy , Aidoo John , Harries Kent A. , Bro William 
Published: February 2010

Abstract
The recently promulgated ASTM D7522 Standard Test Method for Pull-Off Strength for FRP Bonded to Concrete Substrate provides a method for quality control and acceptance testing of fiber reinforced polymer (FRP) systems adhesively bonded to a concrete substrate. In the process of developing ASTM D7522, a number of comments and questions were received—some were incorporated as best practices and some were tabled, requiring further investigation. The present study addresses the latter issues and thereby directs future amendments of the ASTM D7522 standard method. Specifically, this study addresses the effects of specimen shape, the effects of variation in specimen cut depth, methods of cutting square specimens, and the impact of retesting specimens that do not fail during their initial test. It is shown that square specimens should be permitted although their results may not be directly compared with round specimens and they may have some other practical considerations affecting their use. Additionally, it is shown that cutting too deeply into the concrete substrate results in lower values of pull-off strength.
Structure Prediction-Driven Genetics in Saccharomyces cerevisiae Identifies an Interface Between the t-RPA Proteins Stn1 and Ten1
Authors: Paschini Margherita , Mandell Edward K , Lundblad Victoria 
Published: February 2010

Abstract
In Saccharomyces cerevisiae, Cdc13, Stn1, and Ten1 are essential for both chromosome capping and telomere length homeostasis. These three proteins have been proposed to perform their roles at chromosome termini as a telomere-dedicated t-RPA complex, on the basis of several parallels with the conventional RPA complex. In this study, we have used several approaches to test whether a predicted α-helix in the N-terminal domain of the S. cerevisiae Stn1 protein is required for formation of the proposed t-RPA complex, in a manner analogous to the comparable helix in Rpa2. Analysis of a panel of Rpa2–OBStn1 chimeras indicates that whether a chimeric protein contains the Rpa2 or Stn1 version of this α-helix dictates its ability to function in place of Rpa2 or Stn1, respectively. In addition, mutations introduced into a hydrophobic surface of the predicted Stn1 α-helix eliminated association with Ten1. Strikingly, allele-specific suppression of a stn1 mutation in this helix (stn1–L164D) by a ten1 mutation (ten1–D138Y) resulted in a restored Stn1–Ten1 interaction, supporting the identification of a Stn1–Ten1 interface. We conclude that Stn1 interacts with Ten1 through an α-helix, in a manner analogous to the interaction between the comparable subunits of the RPA complex.
Trans Fat Information on Food Labels: Consumer Use and Interpretation
Authors: Ellis Sonya , Glanville N. Theresa 
Published: February 2010

Purpose: Consumers’ use and interpretation of trans fat information on food labels were explored. Methods: Consumers completed an interviewer-administered questionnaire in one of three grocery stores selected purposively to represent geographical location. Data analysis involved examining the relationship of age, gender, grocery shopping habits, household size, and source of nutrition information with awareness, use, and interpretation of trans fat information. Results: Ninety-eight percent (n=239) of participants were aware of trans fat, and most knew of the relationship between trans fat intake and cardiovascular disease. Although the majority of shoppers were aware of the “0 trans fat” nutrition claim on food packages (95%), they were more likely to use the Nutrition Facts panel (60%) to reduce trans fat intake. Men and consumers under age 40 were least likely to be aware of food label information. While most consumers (75%) correctly interpreted the “0 trans fat” nutrition claim and thought foods with this claim could be healthy choices (64%), only 51% purchased these foods to reduce trans fat intake. Conclusions: Nutrition professionals should target messages to reduce trans fat intake at men and consumers under age 40. While general knowledge was good, further education is required to help consumers interpret trans fat information.