Description: Highlights • Code comparisons build confidence in simulators to model interdependent processes. • International hydrate reservoir simulators are compared over five complex problems. • Geomechanical processes significantly impact response of gas hydrate reservoirs. • Simulators yielded comparable results, however many differences are noted. • Equivalent constitutive models are required to achieve agreement across simulators. Geologic reservoirs containing gas hydrate occur beneath permafrost environments and within marine continental slope sediments, representing a potentially vast natural gas source. Numerical simulators provide scientists and engineers with tools for understanding how production efficiency depends on the numerous, interdependent (coupled) processes associated with potential production strategies for these gas hydrate reservoirs. Confidence in the modeling and forecasting abilities of these gas hydrate reservoir simulators (GHRSs) grows with successful comparisons against laboratory and field test results, but such results are rare, particularly in natural settings. The hydrate community recognized another approach to building confidence in the GHRS: comparing simulation results between independently developed and executed computer codes on structured problems specifically tailored to the interdependent processes relevant for gas hydrate-bearing systems. The United States Department of Energy, National Energy Technology Laboratory, (DOE/NETL), sponsored the first international gas hydrate code comparison study, IGHCCS1, in the early 2000s. IGHCCS1 focused on coupled thermal and hydrologic processes associated with producing gas hydrates from geologic reservoirs via depressurization and thermal stimulation. Subsequently, GHRSs have advanced to model more complex production technologies and incorporate geomechanical processes into the existing framework of coupled thermal and hydrologic modeling. This paper contributes to the validation of these recent GHRS developments by providing results from a second GHRS code comparison study, IGHCCS2, also sponsored by DOE/NETL. IGHCCS2 includes participants from an international collection of universities, research institutes, industry, national laboratories, and national geologic surveys. Study participants developed a series of five benchmark problems principally involving gas hydrate processes with geomechanical components. The five problems range from simple geometries with analytical solutions to a representation of the world's first offshore production test of methane hydrates, which was conducted with the depressurization method off the coast of Japan. To identify strengths and limitations in the various GHRSs, study participants submitted solutions for the benchmark problems and discussed differing results via teleconferences. The GHRSs evolved over the course of IGHCCS2 as researchers modified their simulators to reflect new insights, lessons learned, and suggested performance enhancements. The five benchmark problems, final sample solutions, and lessons learned that are presented here document the study outcomes and serve as a reference guide for developing and testing gas hydrate reservoir simulators.

Description: Motivation: All current mitochondrial haplogroup classification tools require variants to be detected from an alignment with the reference sequence and to be properly named according to the canonical nomenclature standards for describing mitochondrial variants, before they can be compared with the haplogroup determining polymorphisms. With the emergence of high-throughput sequencing technologies and hence greater availability of mitochondrial genome sequences, there is a strong need for an automated haplogroup classification tool that is alignment-free and agnostic to reference sequence. Results: We have developed a novel mitochondrial genome haplogroup-defining algorithm using a k-mer approach namely Phy-Mer. Phy-Mer performs equally well as the leading haplogroup classifier, HaploGrep, while avoiding the errors that may occur when preparing variants to required formats and notations. We have further expanded Phy-Mer functionality such that next-generation sequencing data can be used directly as input. Availability and implementation: Phy-Mer is publicly available under the GNU Affero General Public License v3.0 on GitHub ( https://github.com/danielnavarrogomez/phy-mer ). Contact: Xiaowu_Gai@meei.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Background Mitochondrial DNA (mtDNA) diseases are rare disorders whose prevalence is estimated around 1 in 5000. Patients are usually tested only for deletions and for common mutations of mtDNA which account for 5–40% of cases, depending on the study. However, the prevalence of rare mtDNA mutations is not known. Methods We analysed the whole mtDNA in a cohort of 743 patients suspected of manifesting a mitochondrial disease, after excluding deletions and common mutations. Both heteroplasmic and homoplasmic variants were identified using two complementary strategies (Surveyor and MitoChip). Multiple correspondence analyses followed by hierarchical ascendant cluster process were used to explore relationships between clinical spectrum, age at onset and localisation of mutations. Results 7.4% of deleterious mutations and 22.4% of novel putative mutations were identified. Pathogenic heteroplasmic mutations were more frequent than homoplasmic mutations (4.6% vs 2.8%). Patients carrying deleterious mutations showed symptoms before 16 years of age in 67% of cases. Early onset disease (〈1 year) was significantly associated with mutations in protein coding genes (mainly in complex I) while late onset disorders (〉16 years) were associated with mutations in tRNA genes. MTND5 and MTND6 genes were identified as ‘hotspots’ of mutations, with Leigh syndrome accounting for the large majority of associated phenotypes. Conclusions Rare mitochondrial DNA mutations probably account for more than 7.4% of patients with respiratory chain deficiency. This study shows that a comprehensive analysis of mtDNA is essential, and should include young children, for an accurate diagnosis that is now accessible with the development of next generation sequencing technology.

Description: Optical nanoantennas provide a promising pathway toward advanced manipulation of light waves, such as directional scattering, polarization conversion, and fluorescence enhancement. Although these functionalities were mainly studied for nanoantennas in free space or on homogeneous substrates, their integration with optical waveguides offers an important "wired" connection to other functional optical components. Taking advantage of the nanoantenna’s versatility and unrivaled compactness, their imprinting onto optical waveguides would enable a marked enhancement of design freedom and integration density for optical on-chip devices. Several examples of this concept have been demonstrated recently. However, the important question of whether nanoantennas can fulfill functionalities for high-bit rate signal transmission without degradation, which is the core purpose of many integrated optical applications, has not yet been experimentally investigated. We introduce and investigate directional, polarization-selective, and mode-selective on-chip nanoantennas integrated with a silicon rib waveguide. We demonstrate that these nanoantennas can separate optical signals with different polarizations by coupling the different polarizations of light vertically to different waveguide modes propagating into opposite directions. As the central result of this work, we show the suitability of this concept for the control of optical signals with ASK (amplitude-shift keying) NRZ (nonreturn to zero) modulation [10 Gigabit/s (Gb/s)] without significant bit error rate impairments. Our results demonstrate that waveguide-integrated nanoantennas have the potential to be used as ultra-compact polarization-demultiplexing on-chip devices for high–bit rate telecommunication applications.

Description: Author(s): Zheng Gai, X.-G. Zhang, Ivan I. Kravchenko, Scott T. Retterer, and J. F. Wendelken [Phys. Rev. B 85, 024401] Published Tue Jan 03, 2012

Description: The storm water causes the flood in urban area, and it could be treated as a special water resource in storm water management which could be divided into three development phases. The urban storm water management systems are analysed in this paper. The methods estimating the benefit of storm water management including benefit identification, index system and estimate method are introduced.

Description: In this paper, composite films composed of soya bean protein isolate (SPI) and polyacrylamide (PAM) were prepared under variations of ultrasonic power, treatment time and heating temperature. The effects of the major processing parameters related to ultrasonic-assisted treatment were evaluated and optimized through the single-factor analysis and Box–Behnken design (BBD), respectively, when the tensile strength of composite films was considered as the response value. The single-factor analysis was carried out to study the effects of ultrasonic power, treatment time and heating temperature on the viscosity and cohesion of the slurry and the tensile strength of SPI/PAM composite films, which also provided a reasonable data range of each factor for further optimization. Experiment results indicated that these three factors play a significant role in the tensile strength of films. Then BBD was applied to optimize the treatment conditions of these three factors, using the tensile strength of films as the response value. According to the interactive second-order polynomial model of three factors and the three-dimensional response surface, the maximum tensile strength of films was obtained under the optimal condition. To verify the reliability of the model, the experiment with the optimal condition was conducted, and results demonstrated that the observed tensile strength was in agreement with the predicated one. Also, the morphology and water solubility of the films showed that the film can be coated on the yarns evenly and removed clearly.

Description: Author(s): T. Z. Ward, Z. Gai, X. Y. Xu, H. W. Guo, L. F. Yin, and J. Shen In strongly correlated electronic systems, the global transport behavior depends sensitively on spin ordering. We show that spin ordering in manganites can be controlled by depositing isolated ferromagnetic nanodots at the surface. The exchange field at the interface is tunable with nanodot density ... [Phys. Rev. Lett. 106, 157207] Published Thu Apr 14, 2011

Description: Sorafenib ameliorates bleomycin-induced pulmonary fibrosis: potential roles in the inhibition of epithelial–mesenchymal transition and fibroblast activation Cell Death and Disease 4, e665 (June 2013). doi:10.1038/cddis.2013.154 Authors: Y-L Chen, X Zhang, J Bai, L Gai, X-L Ye, L Zhang, Q Xu, Y-X Zhang, L Xu, H-P Li & X Ding

Description: Article Organic materials potentially offer a low-cost, flexible and environment-friendly route to spintronics. Here, the authors demonstrate an organic spin-valve device in which an electric field can control both the magnitude and the sign of magnetoresistance. Nature Communications doi: 10.1038/ncomms5396 Authors: Dali Sun, Mei Fang, Xiaoshan Xu, Lu Jiang, Hangwen Guo, Yanmei Wang, Wenting Yang, Lifeng Yin, Paul C. Snijders, T. Z. Ward, Zheng Gai, X.-G. Zhang, Ho Nyung Lee, Jian Shen