bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequential change of asymmetric dimethylarginine levels after initiation of peritoneal dialysis in patients with end‐stage renal disease
Authors: LEE KWAN‐HYUN , GIL HYO‐WOOK , YANG JONG‐OH , LEE EUN‐YOUNG , HONG SAE‐YONG 
Published: December 2009

ABSTRACTBackground:  We hypothesized that the asymmetric dimethylarginine (ADMA) metabolism in end‐stage renal disease may be linked to the rate of protein turnover and to the vast pool of amino acids. In order to determine a correlation between the plasma levels of ADMA and the protein catabolic rate, we measured the ADMA levels as well as nutritional markers such as the normalized protein catabolic rate (nPCR) in patients with newly initiated continuous ambulatory peritoneal dialysis (CAPD).Methods:  Twenty‐four patients were recruited for this study. All patients were on the standard CAPD protocol, and followed for at least 1 year. Blood samples were collected at baseline before the initiation of peritoneal dialysis, and every 6 months for 1 year. The blood parameters studied included the serum albumin, total cholesterol, glucose, urea nitrogen, creatinine and ADMA. Peritoneal equilibrium test and measurements of weekly Kt/Vurea and nPCR were performed within 4 weeks of the blood sampling.Results:  The change of ADMA levels over 1 year was positively correlated with that of haemoglobin (r = 0.592, P = 0.002) and nPCR during the same period (r = 0.508, P = 0.026).Conclusion:  The findings of our study suggest that nPCR might influence the change of ADMA levels after initiation of CAPD.
Conserved Motifs within Ebola and Marburg Virus VP40 Proteins Are Important for Stability, Localization, and Subsequent Budding of Virus-Like Particles
Authors: Liu Yuliang , Cocka Luis , Okumura Atsushi , Zhang Yong-An , Sunyer J. Oriol , Harty Ronald N. 
Published: December 2009

ABSTRACT

The filovirus VP40 protein is capable of budding from mammalian cells in the form of virus-like particles (VLPs) that are morphologically indistinguishable from infectious virions. Ebola virus VP40 (eVP40) contains well-characterized overlapping L domains, which play a key role in mediating efficient virus egress. L domains represent only one component required for efficient budding and, therefore, there is a need to identify and characterize additional domains important for VP40 function. We demonstrate here that the
96
LPLGVA
101
sequence of eVP40 and the corresponding
84
LPLGIM
89
sequence of Marburg virus VP40 (mVP40) are critical for efficient release of VP40 VLPs. Indeed, deletion of these motifs essentially abolished the ability of eVP40 and mVP40 to bud as VLPs. To address the mechanism by which the
96
LPLGVA
101
motif of eVP40 contributes to egress, a series of point mutations were introduced into this motif. These mutants were then compared to the eVP40 wild type in a VLP budding assay to assess budding competency. Confocal microscopy and gel filtration analyses were performed to assess their pattern of intracellular localization and ability to oligomerize, respectively. Our results show that mutations disrupting the
96
LPLGVA
101
motif resulted in both altered patterns of intracellular localization and self-assembly compared to wild-type controls. Interestingly, coexpression of either Ebola virus GP-WT or mVP40-WT with eVP40-ΔLPLGVA failed to rescue the budding defective eVP40-ΔLPLGVA mutant into VLPs; however, coexpression of eVP40-WT with mVP40-ΔLPLGIM successfully rescued budding of mVP40-ΔLPLGIM into VLPs at mVP40-WT levels. In sum, our findings implicate the LPLGVA and LPLGIM motifs of eVP40 and mVP40, respectively, as being important for VP40 structure/stability and budding.
The Foamy Virus Genome Remains Unintegrated in the Nuclei of G1/S Phase-Arrested Cells, and Integrase Is Critical for Preintegration Complex Transport into the Nucleus
Authors: Lo Yung-Tsun , Tian Tao , Nadeau Peter E. , Park Jeonghae , Mergia Ayalew 
Published: December 2009

ABSTRACTFoamy viruses are a member of the spumavirus subfamily of retroviruses with unique mechanisms of virus replication. Foamy virus replication is cell cycle dependent; however, the genome is found in the nuclei of cells arrested in the G1/S phase. Despite the presence of genome in the nuclei of growth-arrested cells, there is no viral gene expression, thus explaining its dependency on cell cycle. This report shows that the foamy virus genome remains unintegrated in G1/S phase-arrested cells. The foamy virus genome is detected by confocal microscopy in the nuclei of both dividing and growth-arrested cells. Alu PCR revealed foamy virus-specific DNA amplification from genomic DNA isolated in cycling cells at 24 h postinfection. In arrested cells no foamy virus DNA band was detected in cells harvested at 1 or 7 days after infection, and a very faint band that is significantly less than DNA amplified from cycling cells was observed at day 15. After these cells were arrested at the G1/S phase for 1, 7, or 15 days they were allowed to cycle, at which time foamy virus-specific DNA amplification was readily observed. Taken together, these results suggest that the foamy virus genome persists in nondividing cells without integrating. We have also established evidence for the first time that the foamy virus genome and Gag translocation into the nucleus are dependent on integrase in cycling cells, implicating the role of integrase in transport of the preintegration complex into the nucleus. Furthermore, despite the presence of a nuclear localization signal sequence in Gag, we observed no foamy virus Gag importation into the nucleus in the absence of integrase.
Calculating the potential for within-flight transmission of influenza A (H1N1)
Authors: Wagner Bradley G , Coburn Brian J , Blower Sally 
Published: December 2009

AbstractBackgroundClearly air travel, by transporting infectious individuals from one geographic location to another, significantly affects the rate of spread of influenza A (H1N1). However, the possibility of within-flight transmission of H1N1 has not been evaluated; although it is known that smallpox, measles, tuberculosis, SARS and seasonal influenza can be transmitted during commercial flights. Here we present the first quantitative risk assessment to assess the potential for within-flight transmission of H1N1.MethodsWe model airborne transmission of infectious viral particles of H1N1 within a Boeing 747 using methodology from the field of quantitative microbial risk assessment.ResultsThe risk of catching H1N1 will essentially be confined to passengers travelling in the same cabin as the source case. Not surprisingly, we find that the longer the flight the greater the number of infections that can be expected. We calculate that H1N1, even during long flights, poses a low to moderate within-flight transmission risk if the source case travels First Class. Specifically, 0-1 infections could occur during a 5 hour flight, 1-3 during an 11 hour flight and 2-5 during a 17 hour flight. However, within-flight transmission could be significant, particularly during long flights, if the source case travels in Economy Class. Specifically, two to five infections could occur during a 5 hour flight, 5-10 during an 11 hour flight and 7-17 during a 17 hour flight. If the aircraft is only partially loaded, under certain conditions more infections could occur in First Class than in Economy Class. During a 17 hour flight, a greater number of infections would occur in First Class than in Economy if the First Class Cabin is fully occupied, but Economy class is less than 30% full.ConclusionsOur results provide insights into the potential utility of air travel restrictions on controlling influenza pandemics in the winter of 2009/2010. They show travel by one infectious individual, rather than causing a single outbreak of H1N1, could cause several simultaneous outbreaks. These results imply that, during a pandemic, quarantining passengers who travel in Economy on long-haul flights could potentially be an important control strategy. Notably, our results show that quarantining passengers who travel First Class would be unlikely to be an effective control strategy.
Activation of PKA, p38 MAPK and ERK1/2 by gonadotropins in cumulus cells is critical for induction of EGF-like factor and TACE/ADAM17 gene expression during in vitro maturation of porcine COCs
Authors: Yamashita Yasuhisa , Hishinuma Mitsugu , Shimada Masayuki 
Published: December 2009

Abstract

Objectives
During ovulation, it has been shown that LH stimulus induces the expression of numerous genes via PKA, p38 MAPK, PI3K and ERK1/2 in cumulus cells and granulosa cells. Our recent study showed that EGF-like factor and its protease (TACE/ADAM17) are required for the activation of EGF receptor (EGFR), cumulus expansion and oocyte maturation of porcine cumulus-oocyte complexes (COCs). In the present study, we investigated which signaling pathways are involved in the gene expression of EGF-like factor and in Tace/Adam17 expression in cumulus cells of porcine COC during in vitro maturation.

Methods

Areg, Ereg, Tace/Adam17, Has2, Tnfaip6 and Ptgs2 mRNA expressions were detected in cumulus cells of porcine COCs by RT-PCR. Protein level of ERK1/2 phosphorylation in cultured cumulus cells was analyzed by westernblotting. COCs were visualized using a phase-contrast microscope.

Results
When COCs were cultured with FSH and LH up to 2.5 h, Areg, Ereg and Tace/Adam17 mRNA were expressed in cumulus cells of COCs. Areg, Ereg and Tace/Adam17 gene expressions were not suppressed by PI3K inhibitor (LY294002), whereas PKA inhibitor (H89), p38 MAPK inhibitor (SB203580) and MEK inhibitor (U0126) significantly suppressed these gene expressions. Phosphorylation of ERK1/2, and the gene expression of Has2, Tnfaip6 and Ptgs2 were also suppressed by H89, SB203580 and U0126, however, these negative effects were overcome by the addition of EGF to the medium, but not in the U0126 treatment group.

Conclusion
The results showed that PKA, p38 MAPK and ERK1/2 positively controlled the expression of EGF-like factor and TACE/ADMA17, the latter of which impacts the cumulus expansion and oocyte maturation of porcine COCs via the EGFR-ERK1/2 pathway in cumulus cells.
Social structure, social cognition, and physical activity: A test of four models
Authors: Godin Gaston , Sheeran Paschal , Conner Mark , Bélanger‐Gravel Ariane , Gallani Maria Cecília B. J. , Nolin Bertrand 
Published: December 2009

ObjectiveThis study investigated the combined influence of social structural factors (e.g. income) and cognitions in predicting changes in physical activity. Four models were tested: (a) direct effects (social structural factors influence behaviour controlling for cognitions), (b) mediation (cognitions mediate social structural influence), (c) moderation (social structural factors moderate cognition–behaviour relations), and (d) mediated moderation (cognitions mediate the moderating effects of social structural position).DesignBaseline and 3‐month follow‐up surveys.MethodsA random sample of 1,483 adults completed self‐report measures of physical activity at baseline and 3‐month follow‐up. Measures of age, gender, education, income, material and social deprivation, intention, perceived behavioural control (PBC), and intention stability also were taken.ResultsApart from age, social structural factors exhibited very small or marginal effects on behaviour change, and only education moderated the intention–behaviour relation. In contrast, the magnitude of direct effects of the social cognition variables was comparatively large and intention stability mediated the moderating effect of education.ConclusionsStable intentions and PBC are the key predictors of changes in physical activity. Consequently, our findings would suggest the value of focusing on cognitions rather than social structural variables when modelling the determinants of physical activity.
Dip‐pen nanolithography on SiOx and tissue‐derived substrates: comparison with multiple biological inks
Authors: Kramer Marcus A. , Park Heyjin C. , Ivanisevic Albena 
Published: December 2009

AbstractThere has been extensive interest in the micro and nanoscale manipulation of various substrates in the past few decades. One promising technique is dip‐pen nanolithography which has shown the capability to pattern substrates of all forms including, tissue‐derived substrates. Patterning of tissue‐derived substrates is of particular interest, as it would facilitate studies into controlling cell morphology and cell–substrate interaction. To expand the field into this area both peptides and bioactive collagen‐binding peptide‐linked biomolecules were patterned to the inner collagenous zone of the Bruch's membrane (BM). Collagen‐binding peptide, and extra cellular matrix (ECM) proteins laminin and fibronectin were patterned on the BM and SiOx. The lithographic protocol was facilitated by Triton X‐100 which was used to clean the tissue‐derived construct after harvesting. This produced a collagen‐exposed BM which was more hydrophilic (contact angle 67°±8.49°) surface compared with other cleaning methods but it maintained similar surface roughness (root‐mean‐square) 80±18 nm and collagen exposure. This type of surface can be readily patterned with the chosen inks under lower humidity conditions. SCANNING 32: 30–34, 2010. © 2009 Wiley Periodicals, Inc.
The Use of Lactational Amenorrhea as A Method of Family Planning in Eastern Turkey and Influential Factors
Authors: Türk Rukiye , Terzioǧlu Füsun , Eroǧlu Kafiye 
Published: December 2009

Although the lactational amenorrhea method (LAM) is commonly used for contraception, it frequently fails and pregnancy ensues. This descriptive study was conducted to determine the status of the use of breastfeeding as a method of family planning and the influential factors that may have contributed to the success or failure of LAM. The research sample was comprised of 188 women with 6‐month‐old infants in eastern Turkey. A semistructured interview form was used for data collection in face‐to‐face meetings with the women during visits in their homes. In this study, 34% of the women used LAM to prevent pregnancy after childbirth. However, it was observed that only 17.2% of women using LAM fulfilled the LAM criteria with success, and 82.8% did not fulfill one or more of the LAM criteria. The pregnancy rate of women using this method was 32.8%. Two of the three basic criteria necessary for LAM to be effective were not met by the women: having menses (43.8%) and starting supplemental feeding (70.3%).Prenatal and postnatal counseling services need to be integrated and include information and education about the criteria that are necessary for LAM to be used effectively. These services should be given to women who choose to use LAM for contraception.
Fractal and Image Analysis of the Microvasculature in Normal Intestinal Submucosa and Intestinal Polyps in ApcMin/+ Mice
Authors: Fuseler John W. , Bedenbaugh Adam , Yekkala Krishna , Baudino Troy A. 
Published: December 2009

AbstractTumors are supported by the development of a unique vascular bed. We used fractal dimension (Db) and image analysis to quantify differences in the complexity of the vasculature in normal intestinal submucosa and intestinal polyps. ApcMin/+ mice and wild-type mice were perfused with a curable latex compound, intestines sectioned, and images collected via confocal microscopy. The images were analyzed and area (A), perimeter (P), and integrated optical density (IOD) of the normal and tumor vascular beds were measured. The Db, a quantitative descriptor of morphological complexity, was significantly greater for the polyp vasculature from ApcMin/+ mice than controls. This indicates that the polyp microvasculature is more chaotic than that of the controls, while the IOD and average vascular density values displayed no differences. This suggests the mass of blood volume is equivalent in normal and polyp microvasculature. The lower vascular area-perimeter ratios expressed by the polyp microvasculature suggest it is composed of smaller, more tortuous vessels. These data demonstrate that fractal analysis is applicable for providing a quantitative description of vascular complexity associated with angiogenesis occurring in normal or diseased tissue. Application of Db, IOD, and average density provides a clearer quantification of the complex morphology associated with tissue microvasculature.
Cultivation and quantitative proteomic analyses of acidophilic microbial communities
Authors: Belnap Christopher P , Pan Chongle , VerBerkmoes Nathan C , Power Mary E , Samatova Nagiza F , Carver Rudolf L , Hettich Robert L , Banfield Jillian F 
Published: December 2009

Abstract
Acid mine drainage (AMD), an extreme environment characterized by low pH and high metal concentrations, can support dense acidophilic microbial biofilm communities that rely on chemoautotrophic production based on iron oxidation. Field determined production rates indicate that, despite the extreme conditions, these communities are sufficiently well adapted to their habitats to achieve primary production rates comparable to those of microbial communities occurring in some non-extreme environments. To enable laboratory studies of growth, production and ecology of AMD microbial communities, a culturing system was designed to reproduce natural biofilms, including organisms recalcitrant to cultivation. A comprehensive metabolic labeling-based quantitative proteomic analysis was used to verify that natural and laboratory communities were comparable at the functional level. Results confirmed that the composition and core metabolic activities of laboratory-grown communities were similar to a natural community, including the presence of active, low abundance bacteria and archaea that have not yet been isolated. However, laboratory growth rates were slow compared with natural communities, and this correlated with increased abundance of stress response proteins for the dominant bacteria in laboratory communities. Modification of cultivation conditions reduced the abundance of stress response proteins and increased laboratory community growth rates. The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data
Authors: Salari Keyan , Tibshirani Robert , Pollack Jonathan R. 
Published: December 2009

Abstract
Summary: DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage. However, only a subset of genes with altered dosage exhibit concordant changes in gene expression. This subset is likely to be enriched for oncogenes and tumor suppressor genes, and can be identified by integrating these two layers of genome-scale data. We introduce DNA/RNA-Integrator (DR-Integrator), a statistical software tool to perform integrative analyses on paired DNA copy number and gene expression data. DR-Integrator identifies genes with significant correlations between DNA copy number and gene expression, and implements a supervised analysis that captures genes with significant alterations in both DNA copy number and gene expression between two sample classes.
Availability: DR-Integrator is freely available for non-commercial use from the Pollack Lab at http://pollacklab.stanford.edu/ and can be downloaded as a plug-in application to Microsoft Excel and as a package for the R statistical computing environment. The R package is available under the name ‘DRI’ at http://cran.r-project.org/. An example analysis using DR-Integrator is included as supplemental material.
Contact: ksalari@stanford.edu; pollack1@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
Authors: Zhang Qunyuan , Ding Li , Larson David E. , Koboldt Daniel C. , McLellan Michael D. , Chen Ken , Shi Xiaoqi , Kraja Aldi , Mardis Elaine R. , Wilson Richard K. , Borecki Ingrid B. , Province Michael A. 
Published: December 2009

Abstract
Motivation: DNA copy number aberration (CNA) is a hallmark of genomic abnormality in tumor cells. Recurrent CNA (RCNA) occurs in multiple cancer samples across the same chromosomal region and has greater implication in tumorigenesis. Current commonly used methods for RCNA identification require CNA calling for individual samples before cross-sample analysis. This two-step strategy may result in a heavy computational burden, as well as a loss of the overall statistical power due to segmentation and discretization of individual sample's data. We propose a population-based approach for RCNA detection with no need of single-sample analysis, which is statistically powerful, computationally efficient and particularly suitable for high-resolution and large-population studies.
Results: Our approach, correlation matrix diagonal segmentation (CMDS), identifies RCNAs based on a between-chromosomal-site correlation analysis. Directly using the raw intensity ratio data from all samples and adopting a diagonal transformation strategy, CMDS substantially reduces computational burden and can obtain results very quickly from large datasets. Our simulation indicates that the statistical power of CMDS is higher than that of single-sample CNA calling based two-step approaches. We applied CMDS to two real datasets of lung cancer and brain cancer from Affymetrix and Illumina array platforms, respectively, and successfully identified known regions of CNA associated with EGFR, KRAS and other important oncogenes. CMDS provides a fast, powerful and easily implemented tool for the RCNA analysis of large-scale data from cancer genomes.
Availability: The R and C programs implementing our method are available at https://dsgweb.wustl.edu/qunyuan/software/cmds.
Contact: qunyuan@wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The association of –262C/T polymorphism in the catalase gene and delayed graft function of kidney allografts
Authors: DUTKIEWICZ GRAZYNA , DOMANSKI LESZEK , BINCZAK‐KULETA AGNIESZKA , PAWLIK ANDRZEJ , SAFRANOW KRZYSZTOF , CIECHANOWICZ ANDRZEJ , DZIEDZIEJKO VIOLETTA , CIECHANOWSKI KAZIMIERZ 
Published: December 2009

ABSTRACTBackground:  Catalase is an intracellular antioxidant enzyme that is mainly located in cellular peroxisomes and in the cytosol. This enzyme plays a significant role in the development of tolerance to oxidative stress in the adaptive response of cells and tissues. The aim of the present study was to examine the association between the –262C/T polymorphism in the catalase gene and delayed graft function (DGF), acute rejection and chronic allograft nephropathy of kidney allografts.Methods:  One hundred eighty‐seven recipients of first renal transplants were included in the study. The histories of the patients were analysed regarding DGF, acute rejection and chronic allograft nephropathy. The polymorphism –262C/T in the catalase gene was analysed using the polymerase chain reaction – restriction fragment length polymorphism (PCR‐RFLP) method.Results:  The risk of DGF was significantly lower in T allele carriers compared with CC homozygotes: odds ratio = 0.34, 95% confidence interval = 0.17–0.67, P = 0.001. There were no statistically significant associations between the studied polymorphism and acute rejection or chronic allograft nephropathy.Conclusion:  The results of this study suggest that –262C/T polymorphism in the catalase gene is associated with DGF in kidney allograft recipients.