Dynamic Fano Resonance of Quasienergy Excitons in Superlattices

The dynamic Fano resonance (DFR) between discrete quasienergy excitons and sidebands of their ionization continua is predicted and investigated in dc- and ac-driven semiconductor superlattices. This DFR, well controlled by the ac field, delocalizes the excitons and opens an intrinsic decay channel in nonlinear four-wave mixing signals.Comment: 4pages, 4figure

Model-based analysis of two-color arrays (MA2C)

A normalization method based on probe GC content for two-color tiling arrays and an algorithm for detecting peak regions are presented. They are available in a stand-alone Java program

LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes

Legumes play a vital role in maintaining the nitrogen cycle of the biosphere. They conduct symbiotic nitrogen fixation through endosymbiotic relationships with bacteria in root nodules. However, this and other characteristics of legumes, including mycorrhization, compound leaf development and profuse secondary metabolism, are absent in the typical model plant Arabidopsis thaliana. We present LegumeIP (http://plantgrn.noble.org/LegumeIP/), an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes. LegumeIP compiles gene and gene family information, syntenic and phylogenetic context and tissue-specific transcriptomic profiles. The database holds the genomic sequences of three model legumes, Medicago truncatula, Glycine max and Lotus japonicus plus two reference plant species, A. thaliana and Populus trichocarpa, with annotations based on UniProt, InterProScan, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases. LegumeIP also contains large-scale microarray and RNA-Seq-based gene expression data. Our new database is capable of systematic synteny analysis across M. truncatula, G. max, L. japonicas and A. thaliana, as well as construction and phylogenetic analysis of gene families across the five hosted species. Finally, LegumeIP provides comprehensive search and visualization tools that enable flexible queries based on gene annotation, gene family, synteny and relative gene expression

Second harmonic generation and birefringence of some ternary pnictide semiconductors

A first-principles study of the birefringence and the frequency dependent second harmonic generation (SHG) coefficients of the ternary pnictide semiconductors with formula ABC$_2$ (A = Zn, Cd; B = Si, Ge; C = As, P) with the chalcopyrite structures was carried out. We show that a simple empirical observation that a smaller value of the gap is correlated with larger value of SHG is qualitatively true. However, simple inverse power scaling laws between gaps and SHG were not found. Instead, the real value of the nonlinear response is a result of a very delicate balance between different intraband and interband terms.Comment: 13 pages, 12 figure

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

Background: Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type-specific biomarkers. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported. Results: We performed a sequencing-based transcriptional survey of both known long non-coding RNAs and novel intergenic transcripts across a panel of 64 archival tumor samples comprising 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas and sarcomas. We identified hundreds of transcripts from among the known 1,065 long non-coding RNAs surveyed that showed variability in transcript levels between the tumor types and are therefore potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We found that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors. It was shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker. Conclusions: This study provides the first large survey of long non-coding RNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research

Exploring genetic associations with ceRNA regulation in the human genome

Abstract Competing endogenous RNAs (ceRNAs) are RNA molecules that sequester shared microRNAs (miRNAs) thereby affecting the expression of other targets of the miRNAs. Whether genetic variants in ceRNA can affect its biological function and disease development is still an open question. Here we identified a large number of genetic variants that are associated with ceRNA's function using Geuvaids RNA-seq data for 462 individuals from the 1000 Genomes Project. We call these loci competing endogenous RNA expression quantitative trait loci or ‘cerQTL’, and found that a large number of them were unexplored in conventional eQTL mapping. We identified many cerQTLs that have undergone recent positive selection in different human populations, and showed that single nucleotide polymorphisms in gene 3΄UTRs at the miRNA seed binding regions can simultaneously regulate gene expression changes in both cis and trans by the ceRNA mechanism. We also discovered that cerQTLs are significantly enriched in traits/diseases associated variants reported from genome-wide association studies in the miRNA binding sites, suggesting that disease susceptibilities could be attributed to ceRNA regulation. Further in vitro functional experiments demonstrated that a cerQTL rs11540855 can regulate ceRNA function. These results provide a comprehensive catalog of functional non-coding regulatory variants that may be responsible for ceRNA crosstalk at the post-transcriptional level

Molecular portraits of human breast tumours

Human breast tumours are diverse in their natural history and in their responsiveness to treatments1. Variation in transcriptional programs accounts for much of the biological diversity of human cells and tumours. In each cell, signal transduction and regulatory systems transduce information from the cell's identity to its environmental status, thereby controlling the level of expression of every gene in the genome. Here we have characterized variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. These patterns provided a distinctive molecular portrait of each tumour. Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample. Sets of co-expressed genes were identi®ed for which variation in messenger RNA levels could be related to speci®c features of physiological variation. The tumours could be classi®ed into subtypes distinguished by pervasive differences in their gene expression patterns

Implementation of an all-electron GW approximation based on the PAW method without plasmon pole approximation: application to Si, SiC, AlAs, InAs, NaH and KH

A new implementation of the GW approximation (GWA) based on the all-electron Projector-Augmented-Wave method (PAW) is presented, where the screened Coulomb interaction is computed within the Random Phase Approximation (RPA) instead of the plasmon-pole model. Two different ways of computing the self-energy are reported. The method is used successfully to determine the quasiparticle energies of six semiconducting or insulating materials: Si, SiC, AlAs, InAs, NaH and KH. To illustrate the novelty of the method the real and imaginary part of the frequency-dependent self-energy together with the spectral function of silicon are computed. Finally, the GWA results are compared with other calculations, highlighting that all-electron GWA results can differ markedly from those based on pseudopotential approaches.Comment: 11pages,3figures, submitted to PR