Bioinformatic discovery of microRNA precursors from human ESTs and introns

BACKGROUND: MicroRNAs (miRNAs) function in many physiological processes, and their discovery is beneficial for further studying their physiological functions. However, many of the miRNAs predicted from genomic sequences have not been experimentally validated to be authentic expressed RNA transcripts, thereby decreasing the reliability of miRNA discovery. To overcome this problem, we examined expressed transcripts – ESTs and intronic sequences – to identify novel miRNAs as well as their target genes. RESULTS: To facilitate our approach, we developed our scanning method using criteria based on the features of 207 known human pre-miRNAs to discriminate miRNAs from random sequences. We identified 208 candidate hairpins in human ESTs and human reference gene intronic sequences, 52 of which are known pre-miRNAs. The discovery pipeline performance was further assessed using 130 newly updated pre-miRNA and randomly selected sequences. We achieved sensitivity of 85% (110/130) and overall specificity of 49.7% using this method. Because miRNAs are evolutionarily conserved regulators of gene expression, it is expected that their host genes and target genes should have respective phylogenetic orthologs. Our results confirmed that, in certain mammals, the host genes carrying the same miRNAs are orthologs, as previously reported. Moreover, this observation is also the case for some of the miRNA target genes. CONCLUSION: We have predicted 208 human pre-miRNA candidates and over 10,000 putative human target genes. Using sequence information from ESTs and introns ensures that the predicted pre-miRNA candidates are expressed and the combined expression transcription information from ESTs and introns makes our prediction results more decisive with regard to expressed pre-miRNAs

Temperature-dependent Mollow triplet spectra from a single quantum dot: Rabi frequency renormalisation and sideband linewidth insensitivity

We investigate temperature-dependent resonance fluorescence spectra obtained from a single self-assembled quantum dot. A decrease of the Mollow triplet sideband splitting is observed with increasing temperature, an effect we attribute to a phonon-induced renormalisation of the driven dot Rabi frequency. We also present first evidence for a non-perturbative regime of phonon coupling, in which the expected linear increase in sideband linewidth as a function of temperature is cancelled by the corresponding reduction in Rabi frequency. These results indicate that dephasing in semiconductor quantum dots may be less sensitive to changes in temperature than expected from a standard weak-coupling analysis of phonon effects.Comment: Close to published version, new figure and minor changes to the text. 5 pages, 3 figure

Time-resolved boson sampling with photons of different colors

Interference of multiple photons via a linear-optical network has profound applications for quantum foundation, quantum metrology and quantum computation. Particularly, a boson sampling experiment with a moderate number of photons becomes intractable even for the most powerful classical computers, and will lead to "quantum supremacy". Scaling up from small-scale experiments requires highly indistinguishable single photons, which may be prohibited for many physical systems. Here we experimentally demonstrate a time-resolved version of boson sampling by using photons not overlapping in their frequency spectra from three atomic-ensemble quantum memories. Time-resolved measurement enables us to observe nonclassical multiphoton correlation landscapes. An average fidelity over several interferometer configurations is measured to be 0.936(13), which is mainly limited by high-order events. Symmetries in the landscapes are identified to reflect symmetries of the optical network. Our work thus provides a route towards quantum supremacy with distinguishable photons.Comment: 5 pages, 3 figures, 1 tabl

DeltaFS: Pursuing Zero Update Overhead via Metadata-Enabled Delta Compression for Log-structured File System on Mobile Devices

Data compression has been widely adopted to release mobile devices from intensive write pressure. Delta compression is particularly promising for its high compression efficacy over conventional compression methods. However, this method suffers from non-trivial system overheads incurred by delta maintenance and read penalty, which prevents its applicability on mobile devices. To this end, this paper proposes DeltaFS, a metadata-enabled Delta compression on log-structured File System for mobile devices, to achieve utmost compressing efficiency and zero hardware costs. DeltaFS smartly exploits the out-of-place updating ability of Log-structured File System (LFS) to alleviate the problems of write amplification, which is the key bottleneck for delta compression implementation. Specifically, DeltaFS utilizes the inline area in file inodes for delta maintenance with zero hardware cost, and integrates an inline area manage strategy to improve the utilization of constrained inline area. Moreover, a complimentary delta maintenance strategy is incorporated, which selectively maintains delta chunks in the main data area to break through the limitation of constrained inline area. Experimental results show that DeltaFS substantially reduces write traffics by up to 64.8\%, and improves the I/O performance by up to 37.3\%