bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNA and gene expression patterns in the differentiation of human embryonic stem cells
Authors: Ren Jiaqiang , Jin Ping , Wang Ena , Marincola Francesco M , Stroncek David F 
Published: March 2009

Abstract

Background
The unique features of human embryonic stem (hES) cells make them the best candidate resource for both cell replacement therapy and development research. However, the molecular mechanisms responsible for the simultaneous maintenance of their self-renewal properties and undifferentiated state remain unclear. Non-coding microRNAs (miRNA) which regulate mRNA cleavage and inhibit encoded protein translation exhibit temporal or tissue-specific expression patterns and they play an important role in development timing.

Results
In this study, we analyzed miRNA and gene expression profiles among samples from 3 hES cell lines (H9, I6 and BG01v), differentiated embryoid bodies (EB) derived from H9 cells at different time points, and 5 adult cell types including Human Microvascular Endothelial Cells (HMVEC), Human Umbilical Vein Endothelial Cells (HUVEC), Umbilical Artery Smooth Muscle Cells (UASMC), Normal Human Astrocytes (NHA), and Lung Fibroblasts (LFB). This analysis rendered 104 miRNAs and 776 genes differentially expressed among the three cell types. Selected differentially expressed miRNAs and genes were further validated and confirmed by quantitative real-time-PCR (qRT-PCR). Especially, members of the miR-302 cluster on chromosome 4 and miR-520 cluster on chromosome 19 were highly expressed in undifferentiated hES cells. MiRNAs in these two clusters displayed similar expression levels. The members of these two clusters share a consensus 7-mer seed sequence and their targeted genes had overlapping functions. Among the targeted genes, genes with chromatin structure modification function are enriched suggesting a role in the maintenance of chromatin structure. We also found that the expression level of members of the two clusters, miR-520b and miR-302c, were negatively correlated with their targeted genes based on gene expression analysis

Conclusion
We identified the expression patterns of miRNAs and gene transcripts in the undifferentiation of human embryonic stem cells; among the miRNAs that are highly expressed in undifferentiated embryonic stem cells, the miR-520 cluster may be closely involved in hES cell function and its relevance to chromatin structure warrants further study.
Size-partitioning of an urban aerosol to identify particle determinants involved in the proinflammatory response induced in airway epithelial cells
Authors: Ramgolam Kiran , Favez Olivier , Cachier Hélène , Gaudichet Annie , Marano Francelyne , Martinon Laurent , Baeza-Squiban Armelle 
Published: March 2009

Abstract

Background
The contribution of air particles in human cardio-respiratory diseases has been enlightened by several epidemiological studies. However the respective involvement of coarse, fine and ultrafine particles in health effects is still unclear. The aim of the present study is to determine which size fraction from a chemically characterized background aerosol has the most important short term biological effect and to decipher the determinants of such a behaviour.

Results
Ambient aerosols were collected at an urban background site in Paris using four 13-stage low pressure cascade impactors running in parallel (winter and summer 2005) in order to separate four size-classes (PM0.03–0.17 (defined here as ultrafine particles), PM0.17–1 (fine), PM1–2.5(intermediate) and PM2.5–10 (coarse)). Accordingly, their chemical composition and their pro-inflammatory potential on human airway epithelial cells were investigated. Considering isomass exposures (same particle concentrations for each size fractions) the pro-inflammatory response characterized by Granulocyte Macrophage-Colony Stimulating Factor (GM-CSF) release was found to decrease with aerosol size with no seasonal dependency. When cells were exposed to isovolume of particle suspensions in order to respect the particle proportions observed in ambient air, the GM-CSF release was maximal with the fine fraction. In presence of a recombinant endotoxin neutralizing protein, the GM-CSF release induced by particles is reduced for all size-fractions, with exception of the ultra-fine fraction which response is not modified. The different aerosol size-fractions were found to display important chemical differences related to the various contributing primary and secondary sources and aerosol age. The GM-CSF release was correlated to the organic component of the aerosols and especially its water soluble fraction. Finally, Cytochrome P450 1A1 activity that reflects PAH bioavailability varied as a function of the season: it was maximal for the fine fraction in winter and for the ultrafine fraction in summer.

Conclusion
In the frame of future regulations, a particular attention should thus be paid to the ultrafine/fine (here referred to as PM1) fraction due to their overwhelming anthropogenic origin and predominance in the urban aerosol and their pro-inflammatory potential.
Overcoming Resistance to Conventional Drugs in Ewing Sarcoma and Identification of Molecular Predictors of Outcome
Authors: Scotlandi Katia , Remondini Daniel , Castellani Gastone , Manara Maria Cristina , Nardi Filippo , Cantiani Lara , Francesconi Mirko , Mercuri Mario , Caccuri Anna Maria , Serra Massimo , Knuutila Sakari , Picci Piero 
Published: March 2009

Purpose The improvement of Ewing sarcoma (EWS) therapy is currently linked to the discovery of strategies to select patients with poor and good prognosis and of modified treatment regimens. In this study, we analyzed the molecular factors governing EWS response to chemotherapy to identify genetic signatures to be used for risk-adapted therapy. Patients and Methods Microarray technology was used for profiling 30 primary tumors and seven metastases of patients who were classified according to event-free survival. For selected genes, real-time polymerase chain reaction was applied in 42 EWS primary tumors as validation assay. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide test was used to evaluate in vitro drug sensitivity. Results We identified molecular signatures that reflect tumor resistance to chemotherapy. Annotation analysis was applied to reveal the biologic functions that critically influenced clinical outcome. The prognostic relevance of glutathione metabolism pathway was validated. The expression of MGST1, the microsomal glutathione S-transferase (GST), was found to clearly predict EWS prognosis. MGST1 expression was associated with doxorubicin chemosensitivity. This prompted us to assess the in vitro effectiveness of 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX), a new anticancer agent that efficiently inhibits GST enzymes. Six cell lines were found to be sensitive to this new drug. Conclusion Classification of EWS patients into high- and low-risk groups is feasible with restricted molecular signatures that may have practical value at diagnosis for selecting patients with EWS who are unresponsive to current treatments. Glutathione metabolism pathway emerged as one of the most significantly altered prognosis-associated pathway. NBDHEX is proposed as a new potential therapeutic possibility.
Chemoradiotherapy in the Management of Locally Advanced Pancreatic Carcinoma: A Qualitative Systematic Review
Authors: Huguet Florence , Girard Nicolas , Guerche Clotilde Séblain-El , Hennequin Christophe , Mornex Françoise , Azria David 
Published: March 2009

Purpose Pancreatic carcinoma is one of the leading causes of cancer-related mortality. At time of diagnosis, 30% of patients present with a locally advanced unresectable but nonmetastatic pancreatic carcinoma (LAPC). The French program Standards, Options, and Recommendations was promoted to conduct a qualitative systematic review to evaluate the role of radiotherapy in patients with LAPC. Methods A search to identify eligible studies was undertaken using the MEDLINE database. All phase III randomized trials and systematic reviews evaluating the role of radiotherapy in LAPC were included, together with some noncontrolled studies if no phase III trials were retrieved. The quality and clinical relevance of the studies were evaluated using validated checklists, which allowed associating each result with a level of evidence. Results Twenty-one studies were included, as follows: two meta-analyses, 13 randomized trials, and six nonrandomized trials. Chemoradiotherapy increases overall survival when compared with best supportive care (level of evidence C) or with exclusive radiotherapy (level B1), but is more toxic (level B1). Chemoradiotherapy is not superior to chemotherapy in terms of survival (level B1) and increases toxicity (level A). Recent data favor limited irradiation to the tumor volume (level C). Fluorouracil is still the reference chemotherapy in association with radiotherapy (level B1). Induction chemotherapy before chemoradiotherapy improves survival (level C). Conclusion No standard treatment exists, but there are two options for treatment of LAPC; these are gemcitabine-based chemotherapy and chemoradiotherapy. Induction chemotherapy followed by a chemoradiotherapy is a promising strategy for selection of patients without early metastatic/progressing disease.
Convective Mass Transfer Coefficients for Gypsum and Wood Paneling
Authors: Iskra Conrad R. , James Chris , Talukdar Prabal , Simonson Carey J. 
Published: March 2009

Abstract
This paper presents the measured convective mass transfer coefficients for humid air flowing above an initially dry gypsum and wood panel (equilibrium with 30 % RH air) in the transient moisture transfer (TMT) facility at the University of Saskatchewan. The convective coefficients are measured during laminar flow at three different Reynolds numbers (Re=800, 1500, and 2100) and with three different humidities in the air stream (50, 70, and 90 % RH). The results show that the measured mass transfer coefficients are lower than the values measured above an open water surface by Iskra and Simonson in a previous work. For gypsum, the convective mass transfer coefficient varies from 0.0016 to 0.0033 m/s (1.2×10−8 to 2.4×10−8 s/m) with 95 % confidence uncertainty bounds ranging from ±20 to ±57 %. For wood, the convective mass transfer coefficient varies from 0.0001 to 0.0008 m/s (9.4×10−10 to 5.7×10−9 s/m) with 95 % confidence uncertainty bounds ranging from ±50 to±300 %. The experimental data are analyzed with a 1-D heat and mass transfer numerical model to check the discrepancy with the experimental data. The uncertainty associated with an indirect determination of mass transfer coefficient is discussed.
Natural Attenuation of Endocrine Disrupting Chemicals in On-Site Domestic Wastewater Treatment Systems
Authors: Gill Laurence , Misstear Bruce , Johnston Paul , O’Luanaigh Niall 
Published: March 2009

Abstract
Groundwater is an important resource in Ireland which is under increasing risk from the burgeoning numbers of decentralized houses and their respective on-site treatment systems which discharge effluent to ground via a number of parallel percolation trenches. The three-dimensional performance of separate percolation areas have been intensively monitored to ascertain the attenuation of selected Endocrine Disruption Compounds (EDCs) from freely draining unsaturated subsoils receiving septic tank effluent and secondary treated effluent. The performance of secondary treatment and tertiary treatment horizontal subsurface flow reed beds was also studied with respect to EDC removal. The study showed that the development of a biomat across the percolation areas receiving secondary treated effluent was muted compared to the site receiving septic tank effluent on which the percolating effluent spread naturally by gravity over a much larger area. In general, the results showed the oestrogens (oestrone, oestrdiaol, ethynyloestradiol, and oestriol) percolating though the unsaturated subsoil were significantly degraded with depth down to very low values (&lt;1 ng/L), with the exception of oestriol in the secondary treated effluent plume which seemed to be more persistent. There appeared to be little or no degradation of oestrogens under the saturated anaerobic conditions in the reed beds. The organic oxygen compound, bisphenol A, was not significantly reduced in the aerobic secondary treatment processes although some degradation was evident with depth through the subsoil in all trenches. Bisphenol A also showed no significant degradation in the reed bed environment. Finally, the study investigated the fate of caffeine (as a potential indicator of on-site effluent) which showed considerable removal in the aerobic subsoil conditions beneath all the trenches compared to little degradation of caffeine in the saturated anaerobic environment of the reed beds.
A New Cotton Fiber Paper Furnish
Authors: Harpham JA 
Published: March 2009

Cotton fibers possess properties which make them desirable as a papermaking furnish. One type of cotton fiber (that is, linters) has the shortcoming of developing low paper strength and high paper bulk. Chemical modification of the linters fiber eliminates these disadvantages. Paper made from hydroxyethylated linters, in particular, has improved strength, uniform formation, excellent permanency, improved surface characteristics, and new combinations of porosity and absorbency with strength.
Bond, ledger, social, printing, thin, and porous papers are all likely to contain hydroxyethylated cotton linters. For identification of this new fiber, Herzberg iodine stain is inadequate. The microscopical study of morphological characteristics constitutes a preferred basis for fiber characterization. Hydroxyethylated linters may be distinguished from regular linters by determining solubility in alkali. Pulp crystallinity and degree of substitution data provide information, if desired, as to the stage of processing at which the fiber was modified and the extent of modification.
Centrifuge Sedimentation Size Analysis of Samples of Airborne Dusts Collected in Membrane Filters
Authors: Whitby KT , Algren AB , Annis JC 
Published: March 2009

The application of the rapid general purpose centrifuge sedimentation method developed at the University of Minnesota to the size analysis of fine powders has been described in a previous publication (2).
Through the development of special fine-bore capillary centrifuge tubes, this method has been extended to the size analysis of fractional milligram quantities of airborne dusts collected on 47-mm membrane filters. Evaluation of this method against light and electron microscope data and its extensive use in an airborne dust survey have shown that it is a practical and convenient tool for the size analysis of airborne dusts. Application of this method to the size analysis of airborne dusts and of very fine, dilute suspensions of particles in a liquid is also described.
The Stanford Research Institute Particle Bank
Authors: Cadle RD , Thuman W 
Published: March 2009

Research workers in the fine particle field often spend weeks or months preparing samples of particulate material for their research. The material may have special characteristics with respect to particle size, size distribution, density, and other properties. A large part of the sample preparation involves determining the properties of the sample. When a particular investigation is concluded, the samples may be of no further use to the man who prepared them but may be of considerable use to others working in the fine particle field. Early in 1956 the Institute established a particle bank to serve as a depository for such samples and to make them available to any investigator who might need them.
This paper describes the response to the original questionnaires that were sent out prior to the establishment of the bank, types of samples which have been submitted, and numbers and types of requests for samples that have been received. A number of the samples for the particle bank have been analyzed for particle size or particle size distribution by different methods, and the comparative data are supplied.
Judging from the activity of the bank, it is filling a real need in the fine particle field and it is expected that its usefulness will increase as it becomes better known and as a larger supply of samples is accumulated through future years.
Examples of Highway Soil Engineering
Authors: Barber ES 
Published: March 2009

Use of soil engineering in highways is illustrated by a variety of examples from experience on turnpikes and interstate and overseas highways.
Various screening tests to supplement routine classification are suggested, as well as methods of indicating mica content and degree of nonplasticity.
Examples are presented illustrating weathering, intrusion, special considerations in compaction and pavement design, sand drains for slopes and acceleration of swelling, secondary consolidation, bearing capacity on slopes, stability of fissured clay, fills on soft soil and abutment displacement.
Problems of management and education are considered. Relation of soil to other materials is illustrated by grading requirements, shrinkage of asphalt, and swelling of masonry.
Laboratory Methods of Compacting Granular Soils
Authors: Felt EJ 
Published: March 2009

Control of compaction of cohesionless granular soils is frequently confounded by the lack of adequate test methods. These materials do not compact satisfactorily in the standard moisture-density test, ASTM Method D 698. Thus, methods of soil-compaction control based upon the standard density test, which are appropriate for cohesive-type soils, have been found to be unworkable with many cohesionless soils.
It is the assignment of Section D of Subcommittee R-3 of ASTM Committee D-18 to establish tentative ASTM methods for determining the maximum and minimum densities of granular materials. These methods will provide a means for controlling compaction of granular materials based upon either “per cent-compaction” or “relative-density” specifications.
This report presents maximum and minimum density data obtained for six granular materials by eight cooperating committee members, each using test methods of his own choice. The committee expects to select two or three methods for further check testing and ultimately to propose methods for publication as tentative ASTM standards.
Selection for Chaperone-Like Mediated Genetic Robustness at Low Mutation Rate: Impact of Drift, Epistasis and Complexity
Authors: Gros Pierre-Alexis , Tenaillon Olivier 
Published: March 2009

AbstractGenetic robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Overexpression of chaperones, to assist the folding of proteins carrying deleterious mutations, is so far one of the most accepted molecular mechanisms enhancing genetic robustness. Most theories on the evolution of robustness have focused on the implications of high mutation rate. Here we show that genetic drift, which is modulated by population size, organism complexity, and epistasis, can be a sufficient force to select for chaperone-mediated genetic robustness. Using an exact analytical solution, we also show that selection for costly genetic robustness leads to a paradox: the decrease of population fitness on long timescales and the long-term dependency on robustness mechanisms. We suggest that selection for genetic robustness could be universal and not restricted to high mutation rate organisms such as RNA viruses. The evolution of the endosymbiont Buchnera illustrates this selection mechanism and its paradox: the increased dependency on chaperones mediating genetic robustness. Our model explains why most chaperones might have become essential even in optimal growth conditions.
Quantifying Interactions Within the NADP(H) Enzyme Network in Drosophila melanogaster
Authors: Merritt Thomas J S , Kuczynski Caitlin , Sezgin Efe , Zhu Chen-Tseh , Kumagai Seiji , Eanes Walter F 
Published: March 2009

Abstract
In this report, we use synthetic, activity-variant alleles in Drosophila melanogaster to quantify interactions across the enzyme network that reduces nicotinamide adenine dinucleotide phosphate (NADP) to NADPH. We examine the effects of large-scale variation in isocitrate dehydrogenase (IDH) or glucose-6-phosphate dehydrogenase (G6PD) activity in a single genetic background and of smaller-scale variation in IDH, G6PD, and malic enzyme across 10 different genetic backgrounds. We find significant interactions among all three enzymes in adults; changes in the activity of any one source of a reduced cofactor generally result in changes in the other two, although the magnitude and directionality of change differs depending on the gene and the genetic background. Observed interactions are presumably through cellular mechanisms that maintain a homeostatic balance of NADPH/NADP, and the magnitude of change in response to modification of one source of reduced cofactor likely reflects the relative contribution of that enzyme to the cofactor pool. Our results suggest that malic enzyme makes the largest single contribution to the NADPH pool, consistent with the results from earlier experiments in larval D. melanogaster using naturally occurring alleles. The interactions between all three enzymes indicate functional interdependence and underscore the importance of examining enzymes as components of a network.
Minimal Effect of Ectopic Gene Conversion Among Recent Duplicates in Four Mammalian Genomes
Authors: McGrath Casey L , Casola Claudio , Hahn Matthew W 
Published: March 2009

AbstractGene conversion between duplicated genes has been implicated in homogenization of gene families and reassortment of variation among paralogs. If conversion is common, this process could lead to errors in gene tree inference and subsequent overestimation of rates of gene duplication. After performing simulations to assess our power to detect gene conversion events, we determined rates of conversion among young, lineage-specific gene duplicates in four mammal species: human, rhesus macaque, mouse, and rat. Gene conversion rates (number of conversion events/number of gene pairs) among young duplicates range from 8.3% in macaque to 18.96% in rat, including a 5% false-positive rate. For all lineages, only 1–3% of the total amount of sequence examined was converted. There is no increase in GC content in conversion tracts compared to flanking regions of the same genes nor in conversion tracts compared to the same region in nonconverted gene-family members, suggesting that ectopic gene conversion does not significantly alter nucleotide composition in these duplicates. While the majority of gene duplicate pairs reside on different chromosomes in mammalian genomes, the majority of gene conversion events occur between duplicates on the same chromosome, even after controlling for divergence between duplicates. Among intrachromosomal duplicates, however, there is no correlation between the probability of conversion and physical distance between duplicates after controlling for divergence. Finally, we use a novel method to show that at most 5–10% of all gene trees involving young duplicates are likely to be incorrect due to gene conversion. We conclude that gene conversion has had only a small effect on mammalian genomes and gene duplicate evolution in general.