302 research outputs found
Master crossover behavior of parachor correlations for one-component fluids
The master asymptotic behavior of the usual parachor correlations, expressing
surface tension as a power law of the density difference
between coexisting liquid and vapor, is analyzed for a
series of pure compounds close to their liquid-vapor critical point, using only
four critical parameters , , and ,
for each fluid.
... The main consequences of these theoretical estimations are discussed in
the light of engineering applications and process simulations where parachor
correlations constitute one of the most practical method for estimating surface
tension from density and capillary rise measurements
Master singular behavior for the Sugden factor of the one-component fluids near their gas-liquid critical point
We present the master (i.e. unique) behavior of the squared capillary length
- so called the Sudgen factor-, as a function of the temperature-like field
along the critical isochore, asymptotically close to the gas-liquid critical
point of twenty (one component) fluids. This master behavior is obtained using
the scale dilatation of the relevant physical fields of the one-component
fluids. The scale dilatation introduces the fluid-dependent scale factors in a
manner analog with the linear relations between physical fields and scaling
fields needed by the renormalization theory applied to the Ising-like
universality class. The master behavior for the Sudgen factor satisfies
hyperscaling and can be asymptotically fitted by the leading terms of the
theoretical crossover functions for the correlation length and the
susceptibility in the homogeneous domain recently obtained from massive
renormalization in field theory. In the absence of corresponding estimation of
the theoretical crossover functions for the interfacial tension, we define the
range of the temperature-like field where the master leading power law can be
practically used to predict the singular behavior of the Sudgen factor in
conformity with the theoretical description provided by the massive
renormalization scheme within the extended asymptotic domain of the
one-component fluid "subclass"
A complete set of nascent transcription rates for yeast genes
The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) and the RNA pol ChIP-on-chip methods we generated a new, more accurate nascent transcription rate dataset. By comparing this dataset with the indirect ones obtained from the mRNA stabilities and mRNA amount datasets, we are able to obtain biological information about posttranscriptional regulation processes and a genomic snapshot of the location of the active transcriptional machinery. We have obtained nascent transcription rates for 4,670 yeast genes. The median RNA polymerase II density in the genes is 0.078 molecules/kb, which corresponds to an average of 0.096 molecules/gene. Most genes have transcription rates of between 2 and 30 mRNAs/hour and less than 1% of yeast genes have >1 RNA polymerase molecule/gene. Histone and ribosomal protein genes are the highest transcribed groups of genes and other than these exceptions the transcription of genes is an infrequent phenomenon in a yeast cell
Embedding mRNA Stability in Correlation Analysis of Time-Series Gene Expression Data
Current methods for the identification of putatively co-regulated genes directly from gene expression time profiles are based on the similarity of the time profile. Such association metrics, despite their central role in gene network inference and machine learning, have largely ignored the impact of dynamics or variation in mRNA stability. Here we introduce a simple, but powerful, new similarity metric called lead-lag R2 that successfully accounts for the properties of gene dynamics, including varying mRNA degradation and delays. Using yeast cell-cycle time-series gene expression data, we demonstrate that the predictive power of lead-lag R2 for the identification of co-regulated genes is significantly higher than that of standard similarity measures, thus allowing the selection of a large number of entirely new putatively co-regulated genes. Furthermore, the lead-lag metric can also be used to uncover the relationship between gene expression time-series and the dynamics of formation of multiple protein complexes. Remarkably, we found a high lead-lag R2 value among genes coding for a transient complex
The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer
<p>Abstract</p> <p>Background</p> <p>The discordance between steady-state levels of mRNAs and protein has been attributed to posttranscriptional control mechanisms affecting mRNA stability and translation. Traditional methods of genome wide microarray analysis, profiling steady-state levels of mRNA, may miss important mRNA targets owing to significant posttranscriptional gene regulation by RNA binding proteins (RBPs).</p> <p>Methods</p> <p>The ribonomic approach, utilizing RNA immunoprecipitation hybridized to microarray (RIP-Chip), provides global identification of putative endogenous mRNA targets of different RBPs. HuR is an RBP that binds to the AU-rich elements (ARE) of labile mRNAs, such as proto-oncogenes, facilitating their translation into protein. HuR has been shown to play a role in cancer progression and elevated levels of cytoplasmic HuR directly correlate with increased invasiveness and poor prognosis for many cancers, including those of the breast. HuR has been described to control genes in several of the acquired capabilities of cancer and has been hypothesized to be a tumor-maintenance gene, allowing for cancers to proliferate once they are established.</p> <p>Results</p> <p>We used HuR RIP-Chip as a comprehensive and systematic method to survey breast cancer target genes in both MCF-7 (estrogen receptor positive, ER+) and MDA-MB-231 (estrogen receptor negative, ER-) breast cancer cell lines. We identified unique subsets of HuR-associated mRNAs found individually or in both cell types. Two novel HuR targets, <it>CD9 </it>and <it>CALM2 </it>mRNAs, were identified and validated by quantitative RT-PCR and biotin pull-down analysis.</p> <p>Conclusion</p> <p>This is the first report of a side-by-side genome-wide comparison of HuR-associated targets in wild type ER+ and ER- breast cancer. We found distinct, differentially expressed subsets of cancer related genes in ER+ and ER- breast cancer cell lines, and noted that the differential regulation of two cancer-related genes by HuR was contingent upon the cellular environment.</p
Comparison of itraconazole, voriconazole, and posaconazole as oral antifungal prophylaxis in pediatric patients following allogeneic hematopoietic stem cell transplantation
Antifungal prophylaxis with posaconazole vs. fluconazole or itraconazole in pediatric patients with neutropenia
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