ALBERT

Description: Three principal approaches have been proposed for inferring the set of transcripts expressed in RNA samples using RNA-seq. The simplest approach uses curated annotations, which assumes the transcripts in a sample are a subset of the transcripts listed in a curated database. A more ambitious method involves aligning reads to a reference genome and using the alignments to infer the transcript structures, possibly with the aid of a curated transcript database. The most challenging approach is to assemble reads into putative transcripts de novo without the aid of reference data. We have systematically assessed the properties of these three approaches through a simulation study. We have found that the sensitivity of computational transcript set estimation is severely limited. Computational approaches (both genome-guided and de novo assembly) produce a large number of artefacts, which are assigned large expression estimates and absorb a substantial proportion of the signal when performing expression analysis. The approach using curated annotations shows good expression correlation even when the annotations are incomplete. Furthermore, any incorrect transcripts present in a curated set do not absorb much signal, so it is preferable to have a curation set with high sensitivity than high precision. Software to simulate transcript sets, expression values and sequence reads under a wider range of parameter values and to compare sensitivity, precision and signal-to-noise ratios of different methods is freely available online ( https://github.com/boboppie/RSSS ) and can be expanded by interested parties to include methods other than the exemplars presented in this article.

Description: Rock permeability is an important parameter for the formation evaluation. In this paper, a new method with streaming current is proposed to determine the sample permeability based on the electrokinetic effects, and is proved by the experimental measurements. Corresponding to this method, we have designed an experimental setup and a test system, then performed the streaming current (potential) and electro-osmosis pressure experiments with 23 sandstone samples at 0.05 mol l –1 NaCl solution. The streaming current (potential) coefficient and electro-osmosis pressure coefficient are obtained, respectively, with the experimental data at low frequencies with AC lock-in technique. The electrokinetic permeabilities are further calculated with these coefficients. The results are consistent well with the gas permeability measured with Darcy's law, which verifies the current method for estimating rock permeability. Our measurements are also analysed and compared with previous measurements. The results indicate that our method can reflect the essence of electrokinetic effects better and simplify the electrokinetic measurements as well. In addition, we discuss the influences of experimental artefacts (core holder and confining pressure installation) on the electrokinetic data. The results show that the trough phenomenon, appeared in frequency curves of streaming current (potential) coefficients, is induced by the resonance of the core-holder/vibrator system. This is important for the design of electrokinetic setup and the analysis of low-frequency response of the electrokinetic coupling coefficients.

Description: Author(s): Y. W. Cheung, J. Z. Zhang, J. Y. Zhu, W. C. Yu, Y. J. Hu, D. G. Wang, Yuka Otomo, Kazuaki Iwasa, Koji Kaneko, Masaki Imai, Hibiki Kanagawa, Kazuyoshi Yoshimura, and Swee K. Goh The quasiskutterudite superconductor La 3 Co 4 Sn 13 undergoes a phase transition at T * = 152 K. By measuring the temperature dependence of heat capacity, electrical resistivity, and the superlattice reflection intensity using x rays, we explore the character of the phase transition at T * . Our lattice dyna… [Phys. Rev. B 93, 241112(R)] Published Tue Jun 21, 2016

Description: Structural and magnetic properties of many transition-metal dimers embedded in a defected hexagonal boron nitride monolayer are investigated through density functional calculations to search for systems with magnetic anisotropy energies (MAEs) larger than 30meV. In particular, Ir–Ir@Dh–BN is found to have both large MAE (∼126 meV) and high structural stability against dissociation and diffusion, and it hence can serve as magnetic unit in spintronics and quantum computing devices. This giant MAE mainly results from the spin orbit coupling and the magnetization of the upper Ir atom, which is in a rather isolated environment.

Description: In the brain, AMPA-type glutamate receptors are major postsynaptic receptors at excitatory synapses that mediate fast neurotransmission and synaptic plasticity. α/β-Hydrolase domain-containing 6 (ABHD6), a monoacylglycerol lipase, was previously found to be a component of AMPA receptor macromolecular complexes, but its physiological significance in the function of AMPA receptors (AMPARs)...

Description: Epistasis plays an essential role in the development of complex diseases. Interaction methods face common challenge of seeking a balance between persistent power, model complexity, computation efficiency, and validity of identified bio-markers. We introduce a novel W-test to identify pairwise epistasis effect, which measures the distributional difference between cases and controls through a combined log odds ratio. The test is model-free, fast, and inherits a Chi-squared distribution with data adaptive degrees of freedom. No permutation is needed to obtain the P -values. Simulation studies demonstrated that the W-test is more powerful in low frequency variants environment than alternative methods, which are the Chi-squared test, logistic regression and multifactor-dimensionality reduction (MDR). In two independent real bipolar disorder genome-wide associations (GWAS) datasets, the W-test identified significant interactions pairs that can be replicated, including SLIT3-CENPN, SLIT3-TMEM132D, CNTNAP2-NDST4 and CNTCAP2-RTN4R . The genes in the pairs play central roles in neurotransmission and synapse formation. A majority of the identified loci are undiscoverable by main effect and are low frequency variants. The proposed method offers a powerful alternative tool for mapping the genetic puzzle underlying complex disorders.

Description: The relationships between magnetic susceptibility and pedogenic development are different in various regions of the world. For example, loess magnetic susceptibility shows a positive correlation with pedogenic development in Chinese Loess Plateau (CLP), while it displays a negative correlation with pedogenesis in Alaska and Siberia. To better understand the relationship between magnetic properties and pedogenic development, detailed sampling of Dashing Rocks loess section at Timaru, South Island, New Zealand, was carried out. Multiproxy magnetic parameters such as magnetic susceptibility, anhysteretic remanent magnetization, magnetic hysteresis loops, M s – T curves and – T curves were measured. The results show that the types of magnetic minerals are similar to CLP: magnetite, maghemite, goethite and hematite. However, great differences are found in their concentration: most minerals in the Dashing Rocks section are hard magnetic, such as goethite, the content of paramagnetic minerals is rather high, while the soft-magnetic mineral content is very low. Hard-magnetic and paramagnetic minerals increase with depth, but soft-magnetic minerals decrease with depth, and are absent in the lower part of the profile. Gammate soil structures and Fe/Mn nodules (or pans) are commonly observed in the section, indicating that high susceptibility magnetite and maghemite have been converted to goethite and migrated downward to enrich certain horizons during chemical weathering. This process leads to lower magnetic susceptibility values, possibly related to the source and the transformation of soft-magnetic minerals in a high soil moisture environment. The relationship between magnetic susceptibility and pedogenic development in Dashing Rocks loess section is therefore different from the simple positive and negative relationships in CLP and Siberia, respectively. The more complex relationships between magnetic properties and pedogenic development in New Zealand loess may be related to differing degrees of magnetic mineral transformation at different depths and at different times.

Description: Author(s): J. Hu, T. J. Liu, B. Qian, and Z. Q. Mao We have studied the coupling of electronic and magnetic properties in Fe 1+ y (Te 1− x Se x ) via systematic specific heat, magnetoresistivity (MR), and Hall coefficient measurements on two groups of samples with y =0.02 and 0.1. In the y =0.02 series, we find that the 0.09〈 x 〈0.3 composition region, whe... [Phys. Rev. B 88, 094505] Published Mon Sep 09, 2013

Description: Author(s): J. Karel, J. Juraszek, J. Minar, C. Bordel, K. H. Stone, Y. N. Zhang, J. Hu, R. Q. Wu, H. Ebert, J. B. Kortright, and F. Hellman Off-stoichiometry, epitaxial Fe x Si 1−x thin films (0.5〈x〈1.0) exhibit D0 3 or B2 chemical order, even far from stoichiometry. Theoretical calculations show the magnetic moment is strongly enhanced in the fully chemically disordered A2 phase, while both theoretical and experimental results show t... [Phys. Rev. B 91, 144402] Published Mon Apr 06, 2015

Description: Viruses with single-stranded (ss) DNA genomes infect hosts in all three domains of life and include many medically, ecologically, and economically important pathogens. Recently, a new group of ssDNA viruses with chimeric genomes has been discovered through viral metagenomics. These chimeric viruses combine capsid protein genes and replicative protein genes that, respectively, appear to have been inherited from viruses with positive-strand RNA genomes, such as tombusviruses, and ssDNA genomes, such as circoviruses, nanoviruses or geminiviruses. Here, we describe the genome sequence of a new representative of this virus group and reveal an additional layer of chimerism among ssDNA viruses. We show that not only do these viruses encompass genes for capsid proteins and replicative proteins that have distinct evolutionary histories, but also the replicative genes themselves are chimeras of functional domains inherited from viruses of different families. Our results underscore the importance of horizontal gene transfer in the evolution of ssDNA viruses and the role of genetic recombination in the emergence of novel virus groups.