PS-TRUST: Provably Secure Solution for Truthful Double Spectrum Auctions

Truthful spectrum auctions have been extensively studied in recent years. Truthfulness makes bidders bid their true valuations, simplifying greatly the analysis of auctions. However, revealing one's true valuation causes severe privacy disclosure to the auctioneer and other bidders. To make things worse, previous work on secure spectrum auctions does not provide adequate security. In this paper, based on TRUST, we propose PS-TRUST, a provably secure solution for truthful double spectrum auctions. Besides maintaining the properties of truthfulness and special spectrum reuse of TRUST, PS-TRUST achieves provable security against semi-honest adversaries in the sense of cryptography. Specifically, PS-TRUST reveals nothing about the bids to anyone in the auction, except the auction result. To the best of our knowledge, PS-TRUST is the first provably secure solution for spectrum auctions. Furthermore, experimental results show that the computation and communication overhead of PS-TRUST is modest, and its practical applications are feasible.Comment: 9 pages, 4 figures, submitted to Infocom 201

Biased alternative polyadenylation in human tissues

BACKGROUND: Alternative polyadenylation is one of the mechanisms in human cells that give rise to a variety of transcripts from a single gene. More than half of the human genes have multiple polyadenylation sites (poly(A) sites), leading to variable mRNA and protein products. Previous studies of individual genes have indicated that alternative polyadenylation could occur in a tissue-specific manner. RESULTS: We set out to systematically investigate the occurrence and mechanism of alternative polyadenylation in different human tissues using bioinformatic approaches. Using expressed sequence tag (EST) data, we investigated 42 distinct tissue types. We found that several tissues tend to use poly(A) sites that are biased toward certain locations of a gene, such as sites located in introns or internal exons, and various sites in the exon located closest to the 3' end. We also identified several tissues, including eye, retina and placenta, that tend to use poly(A) sites not frequently used in other tissues. By exploring microarray expression data, we analyzed over 20 genes whose protein products are involved in the process or regulation of mRNA polyadenylation. Several brain tissues showed high concordance of gene expression of these genes with each other, but low concordance with other tissue types. By comparing genomic regions surrounding poly(A) sites preferentially used in brain tissues with those in other tissues, we identified several cis-regulatory elements that were significantly associated with brain-specific poly(A) sites. CONCLUSION: Our results indicate that there are systematic differences in poly(A) site usage among human tissues, and both trans-acting factors and cis-regulatory elements may be involved in regulating alternative polyadenylation in different tissues

PolyA_DB: a database for mammalian mRNA polyadenylation

Messenger RNA polyadenylation is one of the key post-transcriptional events in eukaryotic cells. A large number of genes in mammalian species can undergo alternative polyadenylation, which leads to mRNAs with variable 3′ ends. As the 3′ end of mRNAs often contains cis elements important for mRNA stability, mRNA localization and translation, the implications of the regulation of polyadenylation can be multifold. Alternative polyadenylation is controlled by cis elements and trans factors, and is believed to occur in a tissue- or disease-specific manner. Given the availability of many databases devoted to other aspects of mRNA metabolism, such as transcriptional initiation and splicing, systematic information on polyadenylation, including alternative polyadenylation and its regulation, is noticeably lacking. Here, we present a database named polyA_DB, through which we strive to provide several types of information regarding polyadenylation in mammalian species: (i) polyadenylation sites and their locations with respect to the genomic structure of genes; (ii) cis elements surrounding polyadenylation sites; (iii) comparison of polyadenylation configuration between orthologous genes; and (iv) tissue/organ information for alternative polyadenylation sites. Currently, polyA_DB contains 45 565 polyadenylation sites for 25 097 human and mouse genes, representing the most comprehensive polyadenylation database till date. The database is accessible via the website (http://polya.umdnj.edu/polyadb)

A large-scale analysis of mRNA polyadenylation of human and mouse genes

mRNA polyadenylation is a critical cellular process in eukaryotes. It involves 3′ end cleavage of nascent mRNAs and addition of the poly(A) tail, which plays important roles in many aspects of the cellular metabolism of mRNA. The process is controlled by various cis-acting elements surrounding the cleavage site, and their binding factors. In this study, we surveyed genome regions containing cleavage sites [herein called poly(A) sites], for 13 942 human and 11 155 mouse genes. We found that a great proportion of human and mouse genes have alternative polyadenylation (∼54 and 32%, respectively). The conservation of alternative polyadenylation type or polyadenylation configuration between human and mouse orthologs is statistically significant, indicating that alternative polyadenylation is widely employed by these two species to produce alternative gene transcripts. Genes belonging to several functional groups, indicated by their Gene Ontology annotations, are biased with respect to polyadenylation configuration. Many poly(A) sites harbor multiple cleavage sites (51.25% human and 46.97% mouse sites), leading to heterogeneous 3′ end formation for transcripts. This implies that the cleavage process of polyadenylation is largely imprecise. Different types of poly(A) sites, with regard to their relative locations in a gene, are found to have distinct nucleotide composition in surrounding genomic regions. This large-scale study provides important insights into the mechanism of polyadenylation in mammalian species and represents a genomic view of the regulation of gene expression by alternative polyadenylation

Alternative polyadenylation of cyclooxygenase-2

A biologically important human gene, cyclooxygenase-2 (COX-2), has been proposed to be regulated at many levels. While COX-1 is constitutively expressed in cells, COX-2 is inducible and is upregulated in response to many signals. Since increased transcriptional activity accounts for only part of the upregulation of COX-2, we chose to explore other RNA processing mechanisms in the regulation of this gene. We performed a comprehensive bioinformatics survey, the first of its kind known for human COX-2, which revealed that the human COX-2 gene has alternative polyadenylation (proximal and distal sites) and suggested that use of the alternative polyadenylation signals has tissue specificity. We experimentally established this in HepG2 and HT29 cells. We used an in vivo polyadenylation assay to examine the relative strength of the COX-2 proximal and distal polyadenylation signals, and have shown that the proximal polyadenylation signal is much weaker than the distal one. The efficiency of utilization of many suboptimal mammalian polyadenylation signals is affected by sequence elements located upstream of the AAUAAA, known as upstream efficiency elements (USEs). Here, we used in vivo polyadenylation assays in multiple cell lines to demonstrate that the COX-2 proximal polyadenylation signal contains USEs, mutation of the USEs substantially decreased usage of the proximal signal, and that USE spacing relative to the polyadenylation signal was significant. In addition, mutation of the COX-2 proximal polyadenylation signal to a more optimal sequence enhanced polyadenylation efficiency 3.5-fold. Our data suggest for the first time that alternative polyadenylation of COX-2 is an important post-transcriptional regulatory event

Discovery of two new hypervelocity stars from the LAMOST spectroscopic surveys

We report the discovery of two new unbound hypervelocity stars (HVSs) from the LAMOST spectroscopic surveys. They are respectively a B2V type star of ~ 7 M$_{\rm \odot}$ with a Galactic rest-frame radial velocity of 502 km/s at a Galactocentric radius of ~ 21 kpc and a B7V type star of ~ 4 M$_{\rm \odot}$ with a Galactic rest-frame radial velocity of 408 km/s at a Galactocentric radius of ~ 30 kpc. The origins of the two HVSs are not clear given their currently poorly measured proper motions. However, the future data releases of Gaia should provide proper motion measurements accurate enough to solve this problem. The ongoing LAMOST spectroscopic surveys are expected to yield more HVSs to form a statistical sample, providing vital constraint on understanding the nature of HVSs and their ejection mechanisms.Comment: 5 pages, 3 figures, 1 table, accepted for publication in ApJ

Phase unwrapping in optical metrology via denoised and convolutional segmentation networks

The interferometry technique is corn commonly used to obtain the phase information of an object in optical metrology. The obtained wrapped phase is subject to a 27 pi ambiguity. To remove the ambiguity and obtain the correct phase, phase unwrapping is essential. Conventional phase unwrapping approaches are time-consuming and noise sensitive. To address those issues, we propose a new approach, where we transfer the task of phase unwrapping into a multi-class classification problem and introduce an efficient segmentation network to identify classes. Moreover, a noise-to-noise denoised network is integrated to preprocess noisy wrapped phase. We have demonstrated the proposed method with simulated data and in a real interferometric system.China Scholarship Council (CSC) [201704910730]; National Science Foundation (NSF) [1455630]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]