ALBERT

Description: 16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities.

Description: Author(s): C. Stock, C. Broholm, Y. Zhao, F. Demmel, H. J. Kang, K. C. Rule, and C. Petrovic Neutron scattering in strong magnetic fields is used to show the spin resonance in superconducting CeCoIn 5 ( T c =2.3  K) is a doublet. The underdamped resonance ( ℏ Γ =0.069±0.019  meV) Zeeman splits into two modes at E ± = ℏ Ω 0 ± α μ B μ 0 H with α =0.96±0.05. A linear extrapolation of the lower peak reaches zero e... [Phys. Rev. Lett. 109, 167207] Published Wed Oct 17, 2012

Description: Leber's hereditary optic neuropathy (LHON) is the most common mitochondrial disorder. Nuclear modifier genes are proposed to modify the phenotypic expression of LHON-associated mitochondrial DNA (mtDNA) mutations. By using an exome sequencing approach, we identified a LHON susceptibility allele (c.572G〉T, p.191Gly〉Val) in YARS2 gene encoding mitochondrial tyrosyl-tRNA synthetase, which interacts with m.11778G〉A mutation to cause visual failure. We performed functional assays by using lymphoblastoid cell lines derived from members of Chinese families (asymptomatic individuals carrying m.11778G〉A mutation, or both m.11778G〉A and heterozygous p.191Gly〉Val mutations and symptomatic subjects harboring m.11778G〉A and homozygous p.191Gly〉Val mutations) and controls lacking these mutations. The 191Gly〉Val mutation reduced the YARS2 protein level in the mutant cells. The aminoacylated efficiency and steady-state level of tRNA Tyr were markedly decreased in the cell lines derived from patients both carrying homozygous YARS2 p.191Gly〉Val and m.11778G〉A mutations. The failure in tRNA Tyr metabolism impaired mitochondrial translation, especially for polypeptides with high content of tyrosine codon such as ND4, ND5, ND6 and COX2 in cells lines carrying homozygous YARS2 p.191Gly〉Val and m.11778G〉A mutations. The YARS2 p.191Gly〉Val mutation worsened the respiratory phenotypes associated with m.11778G〉A mutation, especially reducing activities of complexes I and IV. The respiratory deficiency altered the efficiency of mitochondrial ATP synthesis and increased the production of reactive oxygen species. Thus, mutated YARS2 aggravates mitochondrial dysfunctions associated with the m.11778G〉A mutation, exceeding the threshold for the expression of blindness phenotype. Our findings provided new insights into the pathophysiology of LHON that were manifested by interaction between mtDNA mutation and mutated nuclear-modifier YARS2 .

Description: Recent works have shown the usefulness of network and application layer protocols that connect low-power sensor nodes directly to multiple applications and users on the Internet. We propose a security solution for this scenario. While previous works have provided security support for various communication patterns in sensor networks, such as among nodes, from nodes to a base station, and from users to nodes, the security of communication from sensor nodes to multiple users has not been sufficiently addressed. Specifically, we explore this design space and develop a security solution, named Secure Tiny Web Service, for efficient authentication of data sent by a resource-constrained sensor node to multiple users, using digital signatures. We investigate the resource overheads in communication and computation of four suitable signature schemes—the Elliptic Curve Digital Signature Algorithm, the (elliptic curve) Schnorr signature, and the Boneh–Lynn–Shacham and Zhang–Safavi-Naini–Susilo short signature schemes. We implement these schemes on two popular sensor node architectures (based on AVR ATmega128L and MSP430 processors with 802.15.4 radios) and experimentally characterize relevant trade-offs.

Description: Author(s): Y. Zhao, F. Andraschko, and J. Sirker We numerically investigate the growth of the entanglement entropy S ent ( t ) in time t , after a global quench from a product state, in quantum chains with various kinds of disorder. The main focus is, in particular, on fermionic chains with bond disorder. In the noninteracting case at criticality we nu… [Phys. Rev. B 93, 205146] Published Wed May 25, 2016

Description: Author(s): L. Z. Deng, B. Lv, K. Zhao, F. Y. Wei, Y. Y. Xue, Z. Wu, and C. W. Chu To explore the origin of the unusual nonbulk superconductivity with a T c up to 49 K reported in the rare-earth-doped CaF e 2 A s 2 , the chemical composition, magnetization, specific heat, resistivity, and annealing effect are systematically investigated on nominal ( C a 1 − x R x ) F e 2 A s 2 single crystals with dif… [Phys. Rev. B 93, 054513] Published Fri Feb 12, 2016

Description: Author(s): J. D. Song, C. Fan, Z. Y. Zhao, F. B. Zhang, J. Y. Zhao, X. G. Liu, X. Zhao, Y. J. Liu, J. F. Wang, and X. F. Sun We report a study of magnetism and magnetic transitions of hexagonal ErMnO 3 single crystals by magnetization, specific heat, and heat transport measurements. Magnetization data show that the c -axis magnetic field induces three magnetic transitions at 0.8, 12, and 28 T. The specific heat shows a peak... [Phys. Rev. B 96, 174425] Published Mon Nov 20, 2017

Description: Service composition has been proven to be a convincing computing paradigm for rapidly constructing large-scale distributed applications within and across organizational boundaries. Quality of service (QoS)-aware service composition, i.e. selection of the optimal execution plan that maximizes the composition's end-to-end QoS properties, is an active area of research and development endeavors in service composition. In this article, we propose an orthogonal genetic algorithm (OGA) for QoS-aware service composition problem. Its significant feature is to incorporate an orthogonal design method into the initial population generation process and crossover operation. As a result, our algorithm is more robust and can search the solution space in a statistically sound manner. We have executed the OGA to solve 81 randomly generated service composition problems with different sizes and structures based on QWS data set including 2507 real Web services. The results indicate that our OGA can find near-optimal solutions within moderate numbers of generation and has the performance superiority in comparison with many existing optimization algorithms.

Description: Author(s): R. J. Koch, M. Weser, W. Zhao, F. Viñes, K. Gotterbarm, S. M. Kozlov, O. Höfert, M. Ostler, C. Papp, J. Gebhardt, H.-P. Steinrück, A. Görling, and Th. Seyller We report on experimental and theoretical investigations of nitrogen-doped graphene. The incorporation of nitrogen was achieved during chemical-vapor deposition on Ni(111) using pyridine as a precursor. The obtained graphene layers were investigated using photoelectron spectroscopy. By studying C 1 s ... [Phys. Rev. B 86, 075401] Published Wed Aug 01, 2012

Description: The Australian numbat, Myrmecobius fasciatus , is the only marsupial that feeds almost exclusively on termites and that has a life following the diurnally restricted and dynamic geographical distribution of termites. The millions of years of this adaptation led to unique morphological and anatomical features, especially basicranial and dental characteristics, that make it difficult to identify a clear phylogenetic affiliation to other marsupials. From DNA sequence analyses, the family Myrmecobiidae is placed within the dasyuromorph marsupials, but the exact position varies from study to study, and support values are mostly rather modest. Here, we report the recovery and analysis of approximately 110,000 quasifossilized traces of mobile element insertions into the genome of a dasyurid marsupial (Tasmanian devil), 25 of which are phylogenetically informative for early dasyuromorphial evolution. Fourteen of these ancient retroposon insertions are shared by the 16 Dasyuromorphia species analyzed, including the numbat, but are absent in the outgroups. An additional 11 other insertions are present in all Dasyuridae but are absent in the numbat. These findings place numbats as the sister group to all living Dasyuridae and show that the investigated Dasyuromorphia, including the Myrmecobiidae, constitutes a monophyletic group that is separated from Peramelemorphia, Notoryctemorphia, and other marsupials.