Integrative analyses of transcriptome sequencing identify novel functional lncRNAs in esophageal squamous cell carcinoma.

Long non-coding RNAs (lncRNAs) have a critical role in cancer initiation and progression, and thus may mediate oncogenic or tumor suppressing effects, as well as be a new class of cancer therapeutic targets. We performed high-throughput sequencing of RNA (RNA-seq) to investigate the expression level of lncRNAs and protein-coding genes in 30 esophageal samples, comprised of 15 esophageal squamous cell carcinoma (ESCC) samples and their 15 paired non-tumor tissues. We further developed an integrative bioinformatics method, denoted URW-LPE, to identify key functional lncRNAs that regulate expression of downstream protein-coding genes in ESCC. A number of known onco-lncRNA and many putative novel ones were effectively identified by URW-LPE. Importantly, we identified lncRNA625 as a novel regulator of ESCC cell proliferation, invasion and migration. ESCC patients with high lncRNA625 expression had significantly shorter survival time than those with low expression. LncRNA625 also showed specific prognostic value for patients with metastatic ESCC. Finally, we identified E1A-binding protein p300 (EP300) as a downstream executor of lncRNA625-induced transcriptional responses. These findings establish a catalog of novel cancer-associated functional lncRNAs, which will promote our understanding of lncRNA-mediated regulation in this malignancy

The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish

The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome.org

Superconductivity at the Border of Electron Localization and Itinerancy

The superconducting state of iron pnictides and chalcogenides exists at the border of antiferromagnetic order. Consequently, these materials could provide clues about the relationship between magnetism and unconventional superconductivity. One explanation, motivated by the so-called bad-metal behaviour of these materials, proposes that magnetism and superconductivity develop out of quasi-localized magnetic moments which are generated by strong electron-electron correlations. Another suggests that these phenomena are the result of weakly interacting electron states that lie on nested Fermi surfaces. Here we address the issue by comparing the newly discovered alkaline iron selenide superconductors, which exhibit no Fermi-surface nesting, to their iron pnictide counterparts. We show that the strong-coupling approach leads to similar pairing amplitudes in these materials, despite their different Fermi surfaces. We also find that the pairing amplitudes are largest at the boundary between electronic localization and itinerancy, suggesting that new superconductors might be found in materials with similar characteristics.Comment: Version of the published manuscript prior to final journal-editting. Main text (23 pages, 4 figures) + Supplementary Information (14 pages, 7 figures, 3 tables). Calculation on the single-layer FeSe is added. Enhancement of the pairing amplitude in the vicinity of the Mott transition is highlighted. Published version is at http://www.nature.com/ncomms/2013/131115/ncomms3783/full/ncomms3783.htm

Dark Matter in the Singlet Extension of MSSM: Explanation of Pamela and Implication on Higgs Phenomenology

As discussed recently by Hooper and Tait, the singlino-like dark matter in the Minimal Supersymmetric Standard Model (MSSM) extended by a singlet Higgs superfield can give a perfect explanation for both the relic density and the Pamela result through the Sommerfeld-enhanced annihilation into singlet Higgs bosons ($a$ or $h$ followed by $h->a a$) with $a$ being light enough to decay dominantly to muons or electrons. In this work we analyze the parameter space required by such a dark matter explanation and also consider the constraints from the LEP experiments. We find that although the light singlet Higgs bosons have small mixings with the Higgs doublets in the allowed parameter space, their couplings with the SM-like Higgs boson $h_{SM}$ (the lightest doublet-dominant Higgs boson) can be enhanced by the soft parameter $A_\kappa$ and, in order to meet the stringent LEP constraints, the $h_{SM}$ tends to decay into the singlet Higgs pairs $aa$ or $hh$ instead of $b\bar b$. So the $h_{SM}$ produced at the LHC will give a multi-muon signal, h_{SM} -> aa -> 4 muons or h_{SM} -> hh -> 4 a -> 8 muons.Comment: Version in JHE

Structure and Dynamics of Superconducting NaxCoO(2) Hydrate and Its Unhydrated Analog

Neutron scattering has been used to investigate the crystal structure and lattice dynamics of superconducting Na0.3CoO2 1.4(H/D)2O, and the parent Na0.3CoO2 material. The structure of Na0.3CoO2 consists of alternate layers of CoO2 and Na and is the same as the structure at higher Na concentrations. For the superconductor, the water forms two additional layers between the Na and CoO2, increasing the c-axis lattice parameter of the hexagonal P63/mmc space group from 11.16 A to 19.5 A. The Na ions are found to occupy a different configuration from the parent compound, while the water forms a structure that replicates the structure of ice. Both types of sites are only partially occupied. The CoO2 layer in these structures is robust, on the other hand, and we find a strong inverse correlation between the CoO2 layer thickness and the superconducting transition temperature (TC increases with decreasing thickness). The phonon density-of-states for Na0.3CoO2 exhibits distinct acoustic and optic bands, with a high-energy cutoff of ~100 meV. The lattice dynamical scattering for the superconductor is dominated by the hydrogen modes, with librational and bending modes that are quite similar to ice, supporting the structural model that the water intercalates and forms ice-like layers in the superconductor.Comment: 14 pages, 7 figures, Phys. Rev. B (in press). Minor changes + two figures removed as requested by refere

Thermopower and thermal conductivity of superconducting perovskite MgCNi3MgCNi_3

The thermopower and thermal conductivity of superconducting perovskite $MgCNi_3$ ($T_c \approx$ 8 K) have been studied. The thermopower is negative from room temperature to 10 K. Combining with the negative Hall coefficient reported previously, the negative thermopower definetly indicates that the carrier in $MgCNi_3$ is electron-type. The nonlinear temperature dependence of thermopower below 150 K is explained by the electron-phonon interaction renormalization effects. The thermal conductivity is of the order for intermetallics, larger than that of borocarbides and smaller than $MgB_2$. In the normal state, the electronic contribution to the total thermal conductivity is slightly larger than the lattice contribution. The transverse magnetoresistance of $MgCNi_3$ is also measured. It is found that the classical Kohler's rule is valid above 50 K. An electronic crossover occures at $T^* \sim 50 K$, resulting in the abnormal behavior of resistivity, thermopower, and magnetoresistance below 50 K.Comment: Revised on 12 September 2001, Phys. Rev. B in pres