Numerical Modeling Of OTEC Thermal Discharges In Coastal Waters

Thermal discharge from industrial outfalls is categorized into two major classes based on their density. First class is the effluent that has a higher density than that of the ambient water body. The second class is the effluent that has a lower density than that of the ambient water body. Due to the effect of several factors such as tides, waves, winds, river discharges, thermal effluents etc., the mixing characteristics of OTEC (Ocean Thermal Energy Conversion) thermal plume is much complicated. In this study we try to identify the mixing and dispersion characteristics of coastal waters to consider their physical properties using a field observation and a three-dimensional numerical modeling with FVM (Finite Volume Method). A plume model and observed CTD data was used to predict the mixing behavior of thermal discharges in coastal waters. The elevation, current, temperature and salinity boundary conditions on the open boundary and thermal effluents at the specific boundary are considered in this study. Various turbulence models have been applied in the numerical model to assess the accuracy of turbulence models in predicting the effluent discharges in submerged outfalls. The model successfully reproduced well known the plume behavior in coastal waters. These works illustrate the challenging nature of OTEC environmental studies. Keywords : Ocean Thermal Energy Conversion, Finite Volume Method, Plume Mode

Histone variant H3.3 stimulates HSP70 transcription through cooperation with HP1γ

Histone variant H3.3 and heterochromatin protein 1γ (HP1γ) are two functional components of chromatin with role in gene transcription. However, the regulations of their dynamics during transcriptional activation and the molecular mechanisms underlying their actions remain poorly understood. Here, we provide evidence that heat shock-induced transcription of the human HSP70 gene is regulated via the coordinated and interdependent action of H3.3 and HP1γ. H3.3 and HP1γ are rapidly co-enriched at the human HSP70 promoters upon heat shock in a manner that closely parallels the initiation of transcription. Knockdown of H3.3 prevents the stable recruitment of HP1γ, inhibits active histone modifications, and attenuates HSP70 promoter activity. Likewise, knockdown of HP1γ leads to the decreased levels of H3.3 in the promoter regions and the repression of HSP70 genes. HP1γ selectively recognizes particular modification states of H3.3 in the nucleosome for its action. Moreover, HP1γ is overexpressed in three representative cancer cell lines, and its knockdown leads to reduction in HSP70 gene transcription and inhibition of cancer cell proliferation. We conclude that the physical and functional interactions between H3.3 and HP1γ make a unique contribution to acute HSP70 transcription and cancer development related to the misregulation of this transcription event

Selective requirement of H2B N-Terminal tail for p14ARF-induced chromatin silencing

The N-terminal tail of histone H2B is believed to be involved in gene silencing, but how it exerts its function remains elusive. Here, we report the biochemical characterization of p14ARF tumor suppressor as a transcriptional repressor that selectively recognizes the unacetylated H2B tails on nucleosomes. The p14ARF–H2B tail interaction is functional, as the antagonistic effect of p14ARF on chromatin transcription is lost upon deletion or acetylation of H2B tails. Gene expression profiling and chromatin immunoprecipitation studies emphasize the significance of H2B deacetylation and p14ARF recruitment in establishing a repressive environment over the cell cycle regulatory genes. Moreover, HDAC1-mediated H2B deacetylation, especially at K20, constitutes an essential step in tethering p14ARF near target promoters. Our results thus reveal a hitherto unknown role of p14ARF in the regulation of chromatin transcription, as well as molecular mechanisms governing the repressive action of p14ARF

A New Method for Solving Monotone Generalized Variational Inequalities

We suggest new dual algorithms and iterative methods for solving monotone generalized variational inequalities. Instead of working on the primal space, this method performs a dual step on the dual space by using the dual gap function. Under the suitable conditions, we prove the convergence of the proposed algorithms and estimate their complexity to reach an -solution. Some preliminary computational results are reported.</p

Vaquita: Fast and Accurate Identification of Structural Variation Using Combined Evidence

Motivation: Comprehensive identification of structural variations (SVs) is a crucial task for studying genetic diversity and diseases. However, it remains challenging. There is only a marginal consensus between different methods, and our understanding of SVs is substantially limited.In general, integration of multiple pieces of evidence including split-read, read-pair, soft-clip, and read-depth yields the best result regarding accuracy. However, doing this step by step is usually cumbersome and computationally expensive. Result: We present Vaquita, an accurate and fast tool for the identification of structural variations, which leverages all four types of evidence in a single program. After merging SVs from split-reads and discordant read-pairs, Vaquita realigns the soft-clipped reads to the selected regions using a fast bit-vector algorithm. Furthermore, it also considers the discrepancy of depth distribution around breakpoints using Kullback-Leibler divergence. Finally, Vaquita provides an additional metric for candidate selection based on voting, and also provides robust prioritization based on rank aggregation. We show that Vaquita is robust in terms of sequencing coverage, insertion size of the library, and read length, and is comparable or even better for the identification of deletions, inversions, duplications, and translocations than state-of-the-art tools, using both simulated and real datasets. In addition, Vaquita is more than eight times faster than any other tools in comparison. Availability: Vaquita is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and can be downloaded at http://github.com/seqan/vaquit

Global and Local Competition between Exogenously Introduced microRNAs and Endogenously Expressed microRNAs

It has been reported that exogenously introduced micro-RNA (exo-miRNA) competes with endogenously expressed miRNAs (endo-miRNAs) in human cells, resulting in a detectable upregulation of mRNAs with endo-miRNA target sites (TSs). However, the detailed mechanisms of the competition between exo- and endo-miRNAs remain uninvestigated. In this study, using 74 microarrays that monitored the whole-transcriptome response after introducing miRNAs or siRNAs into HeLa cells, we systematically examined the derepression of mRNAs with exoand/or endo-miRNA TSs.We quantitatively assessed the effect of the number of endo-miRNA TSs on the degree of mRNA derepression. As a result, we observed that the number of endo-miRNA TSs was significantly associated with the degree of derepression, supporting that the derepression resulted from the competition between exo- and endo-miRNAs. However, when we examined whether the site proficiency of exomiRNA TSs could also influence mRNA derepression, to our surprise, we discovered a strong positive correlation. Our analysis indicates that site proficiencies of both exoand endo-miRNA TSs are important determinants for the degree of mRNA derepression, implying that the derepression of mRNAs in response to exo-miRNA is more complex than that currently perceived. Our observations may lead to a more complete understanding of the detailed mechanisms of the competition between exo- and endo-miRNAs and to a more accurate prediction of miRNA targets. Our analysis also suggests an interesting hypothesis that long 3-UTRs may function as molecular buffer against gene expression regulation by individual miRNAs.1331sciescopuskc

TALEN-based knockout library for human microRNAs

Various technical tools have been developed to probe the functions of microRNAs (miRNAs), yet their application has been limited by low efficacy and specificity. To overcome the limitations, we used transcription activator-like effector nucleases (TALENs) to knock out human miRNA genes. We designed and produced a library of 540 pairs of TALENs for 274 miRNA loci, focusing on potentially important miRNAs. The knockout procedure takes only 2-4 weeks and can be applied to any cell type. As a case study, we generated knockout cells for two related miRNAs, miR-141 and miR-200c, which belong to the highly conserved miR-200 family. Interestingly, miR-141 and miR-200c, despite their overall similarity, suppress largely nonoverlapping groups of targets, thus suggesting that functional miRNA-target interaction requires strict seed-pairing. Our study illustrates the potency of TALEN technology and provides useful resources for miRNA research.144471sciescopu

A New One-Step Iterative Process for Common Fixed Points in Banach Spaces

Abstract We introduce a new one-step iterative process and use it to approximate the common fixed points of two asymptotically nonexpansive mappings through some weak and strong convergence theorems. Our process is computationally simpler than the processes currently being used in literature for the purpose.</p

Existence of Solutions for <inline-formula> <graphic file="1029-242X-2010-968271-i1.gif"/></inline-formula>-Generalized Vector Variational-Like Inequalities

We introduce and study a class of -generalized vector variational-like inequalities and a class of -generalized strong vector variational-like inequalities in the setting of Hausdorff topological vector spaces. An equivalence result concerned with two classes of -generalized vector variational-like inequalities is proved under suitable conditions. By using FKKM theorem, some new existence results of solutions for the -generalized vector variational-like inequalities and -generalized strong vector variational-like inequalities are obtained under some suitable conditions.</p