National Institute of Advanced Industrial Science and Technology

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

Perovskite Photovoltaics For many types of low-cost solar cells, including those using dye-sensitized titania, performance is limited by low open-circuit voltages. Lee et al. (p. 643 , published online 4 October; see the Perspective by Norris and Aydil ) have developed a solid-state cell in which structured films of titania or alumina nanoparticles are solution coated with a lead-halide perovskite layer that acts as the absorber and n-type photoactive layer. These particles are coated with a spirobifluorene organic-hole conductor in a solar cell with transparent oxide and metal contacts. For the alumina particles, power conversion efficiencies of up to 10.9% were obtained.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTransformation of Carbon DioxideToshiyasu Sakakura, Jun-Chul Choi, and Hiroyuki YasudaView Author Information National Institute of Advanced Industrial Science and Technology (AIST), AIST Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan Cite this: Chem. Rev. 2007, 107, 6, 2365–2387Publication Date (Web):June 13, 2007Publication History Received19 December 2006Published online13 June 2007Published inissue 1 June 2007https://pubs.acs.org/doi/10.1021/cr068357uhttps://doi.org/10.1021/cr068357uresearch-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views44266Altmetric-Citations3387LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Alcohols,Catalysts,Ethers,Inorganic carbon compounds,Oxides Get e-Alerts

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

Rapid advances in information technology rely on high-speed and large-capacity nonvolatile memories. A number of alternatives to contemporary Flash memory have been extensively studied to obtain a more powerful and functional nonvolatile memory. We review the current status of one of the alternatives, resistance random access memory (ReRAM), which uses a resistive switching phenomenon found in transition metal oxides. A ReRAM memory cell is a capacitor-like structure composed of insulating or semiconducting transition metal oxides that exhibits reversible resistive switching on applying voltage pulses. Recent advances in the understanding of the driving mechanism are described in light of experimental results involving memory cells composed of perovskite manganites and titanates.

The lithium storage properties of graphene nanosheet (GNS) materials as high capacity anode materials for rechargeable lithium secondary batteries (LIB) were investigated. Graphite is a practical anode material used for LIB, because of its capability for reversible lithium ion intercalation in the layered crystals, and the structural similarities of GNS to graphite may provide another type of intercalation anode compound. While the accommodation of lithium in these layered compounds is influenced by the layer spacing between the graphene nanosheets, control of the intergraphene sheet distance through interacting molecules such as carbon nanotubes (CNT) or fullerenes (C60) might be crucial for enhancement of the storage capacity. The specific capacity of GNS was found to be 540 mAh/g, which is much larger than that of graphite, and this was increased up to 730 mAh/g and 784 mAh/g, respectively, by the incorporation of macromolecules of CNT and C60 to the GNS.

Hexagonal boron nitride (h-BN), a layered material similar to graphite, is a promising dielectric. Monolayer h-BN, so-called "white graphene", has been isolated from bulk BN and could be useful as a complementary two-dimensional dielectric substrate for graphene electronics. Here we report the large area synthesis of h-BN films consisting of two to five atomic layers, using chemical vapor deposition. These atomic films show a large optical energy band gap of 5.5 eV and are highly transparent over a broad wavelength range. The mechanical properties of the h-BN films, measured by nanoindentation, show 2D elastic modulus in the range of 200-500 N/m, which is corroborated by corresponding theoretical calculations.

We demonstrate the efficient chemical vapor deposition synthesis of single-walled carbon nanotubes where the activity and lifetime of the catalysts are enhanced by water. Water-stimulated enhanced catalytic activity results in massive growth of superdense and vertically aligned nanotube forests with heights up to 2.5 millimeters that can be easily separated from the catalysts, providing nanotube material with carbon purity above 99.98%. Moreover, patterned, highly organized intrinsic nanotube structures were successfully fabricated. The water-assisted synthesis method addresses many critical problems that currently plague carbon nanotube synthesis.

Consolidated tables showing an extensive listing of the highest independently confirmed efficiencies for solar cells and modules are presented. Guidelines for inclusion of results into these tables are outlined and new entries since July 2014 are reviewed. Copyright © 2014 John Wiley & Sons, Ltd.

Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.

Metal-organic frameworks (MOFs), also known as porous coordination polymers (PCPs), synthesized by assembling metal ions with organic ligands have recently emerged as a new class of crystalline porous materials. The amenability to design as well as fine-tunable and uniform pore structures makes them promising materials for a variety of applications. Controllable integration of MOFs and functional materials is leading to the creation of new multifunctional composites/hybrids, which exhibit new properties that are superior to those of the individual components through the collective behavior of the functional units. This is a rapidly developing interdisciplinary research area. This review provides an overview of the significant advances in the development of diverse MOF composites reported till now with special emphases on the synergistic effects and applications of the composites. The most widely used and successful strategies for composite synthesis are also presented.

The purpose of this study is to determine whether current video datasets have sufficient data for training very deep convolutional neural networks (CNNs) with spatio-temporal three-dimensional (3D) kernels. Recently, the performance levels of 3D CNNs in the field of action recognition have improved significantly. However, to date, conventional research has only explored relatively shallow 3D architectures. We examine the architectures of various 3D CNNs from relatively shallow to very deep ones on current video datasets. Based on the results of those experiments, the following conclusions could be obtained: (i) ResNet-18 training resulted in significant overfitting for UCF-101, HMDB-51, and ActivityNet but not for Kinetics. (ii) The Kinetics dataset has sufficient data for training of deep 3D CNNs, and enables training of up to 152 ResNets layers, interestingly similar to 2D ResNets on ImageNet. ResNeXt-101 achieved 78.4% average accuracy on the Kinetics test set. (iii) Kinetics pretrained simple 3D architectures outperforms complex 2D architectures, and the pretrained ResNeXt-101 achieved 94.5% and 70.2% on UCF-101 and HMDB-51, respectively. The use of 2D CNNs trained on ImageNet has produced significant progress in various tasks in image. We believe that using deep 3D CNNs together with Kinetics will retrace the successful history of 2D CNNs and ImageNet, and stimulate advances in computer vision for videos. The codes and pretrained models used in this study are publicly available <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .

A new mechanism of the magnetoelectric effect based on the spin supercurrent is theoretically presented in terms of a microscopic electronic model for noncollinear magnets. The electric polarization ${\stackrel{\ensuremath{\rightarrow}}{P}}_{ij}$ produced between the two magnetic moments ${\stackrel{\ensuremath{\rightarrow}}{S}}_{i}$ and ${\stackrel{\ensuremath{\rightarrow}}{S}}_{j}$ is given by $\stackrel{\ensuremath{\rightarrow}}{P}\ensuremath{\propto}{\stackrel{\ensuremath{\rightarrow}}{e}}_{ij}\ifmmode\times\else\texttimes\fi{}({\stackrel{\ensuremath{\rightarrow}}{S}}_{i}\ifmmode\times\else\texttimes\fi{}{\stackrel{\ensuremath{\rightarrow}}{S}}_{j})$ with ${\stackrel{\ensuremath{\rightarrow}}{e}}_{ij}$ being the unit vector connecting the sites $i$ and $j$. Applications to the spiral spin structure and the gauge theoretical interpretation are discussed.

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research. A study from the FANTOM consortium using single-molecule cDNA sequencing of transcription start sites and their usage in human and mouse primary cells, cell lines and tissues reveals insights into the specificity and diversity of transcription patterns across different mammalian cell types. FANTOM5 (standing for functional annotation of the mammalian genome 5) is the fifth major stage of a major international collaboration that aims to dissect the transcriptional regulatory networks that define every human cell type. Two Articles in this issue of Nature present some of the project's latest results. The first paper uses the FANTOM5 panel of tissue and primary cell samples to define an atlas of active, in vivo bidirectionally transcribed enhancers across the human body. These authors show that bidirectional capped RNAs are a signature feature of active enhancers and identify more than 40,000 enhancer candidates from over 800 human cell and tissue samples. The enhancer atlas is used to compare regulatory programs between different cell types and identify disease-associated regulatory SNPs, and will be a resource for studies on cell-type-specific enhancers. In the second paper, single-molecule sequencing is used to map human and mouse transcription start sites and their usage in a panel of distinct human and mouse primary cells, cell lines and tissues to produce the most comprehensive mammalian gene expression atlas to date. The data provide a plethora of insights into open reading frames and promoters across different cell types in addition to valuable annotation of mammalian cell-type-specific transcriptomes.

We report a strategy to expand the pore aperture of metal-organic frameworks (MOFs) into a previously unattained size regime (>32 angstroms). Specifically, the systematic expansion of a well-known MOF structure, MOF-74, from its original link of one phenylene ring (I) to two, three, four, five, six, seven, nine, and eleven (II to XI, respectively), afforded an isoreticular series of MOF-74 structures (termed IRMOF-74-I to XI) with pore apertures ranging from 14 to 98 angstroms. All members of this series have noninterpenetrating structures and exhibit robust architectures, as evidenced by their permanent porosity and high thermal stability (up to 300°C). The pore apertures of an oligoethylene glycol-functionalized IRMOF-74-VII and IRMOF-74-IX are large enough for natural proteins to enter the pores.

We introduce a new method of a biped walking pattern generation by using a preview control of the zero-moment point (ZMP). First, the dynamics of a biped robot is modeled as a running cart on a table which gives a convenient representation to treat ZMP. After reviewing conventional methods of ZMP based pattern generation, we formalize the problem as the design of a ZMP tracking servo controller. It is shown that we can realize such controller by adopting the preview control theory that uses the future reference. It is also shown that a preview controller can be used to compensate the ZMP error caused by the difference between a simple model and the precise multibody model. The effectiveness of the proposed method is demonstrated by a simulation of walking on spiral stairs.

Autophagy is an intracellular degradation system, by which cytoplasmic contents are degraded in lysosomes. Autophagy is dynamically induced by nutrient depletion to provide necessary amino acids within cells, thus helping them adapt to starvation. Although it has been suggested that mTOR is a major negative regulator of autophagy, how it controls autophagy has not yet been determined. Here, we report a novel mammalian autophagy factor, Atg13, which forms a stable approximately 3-MDa protein complex with ULK1 and FIP200. Atg13 localizes on the autophagic isolation membrane and is essential for autophagosome formation. In contrast to yeast counterparts, formation of the ULK1-Atg13-FIP200 complex is not altered by nutrient conditions. Importantly, mTORC1 is incorporated into the ULK1-Atg13-FIP200 complex through ULK1 in a nutrient-dependent manner and mTOR phosphorylates ULK1 and Atg13. ULK1 is dephosphorylated by rapamycin treatment or starvation. These data suggest that mTORC1 suppresses autophagy through direct regulation of the approximately 3-MDa ULK1-Atg13-FIP200 complex.

Although microscopic laws of physics are invariant under the reversal of the arrow of time, the transport of energy and information in most devices is an irreversible process. It is this irreversibility that leads to intrinsic dissipations in electronic devices and limits the possibility of quantum computation. We theoretically predict that the electric field can induce a substantial amount of dissipationless quantum spin current at room temperature, in hole-doped semiconductors such as Si, Ge, and GaAs. On the basis of a generalization of the quantum Hall effect, the predicted effect leads to efficient spin injection without the need for metallic ferromagnets. Principles found here could enable quantum spintronic devices with integrated information processing and storage units, operating with low power consumption and performing reversible quantum computation.

Metal-organic frameworks (MOFs), established as a relatively new class of crystalline porous materials with high surface area, structural diversity, and tailorability, attract extensive interest and exhibit a variety of applications, especially in catalysis. Their permanent porosity enables their inherent superiority in confining guest species, particularly small metal nanoparticles (MNPs), for improved catalytic performance and/or the expansion of reaction scope. This is a rapidly developing interdisciplinary research field. In this review, we provide an overview of significant progress in the development of MNP/MOF composites, including various preparation strategies and characterization methods as well as catalytic applications. Special emphasis is placed on synergistic effects between the two components that result in an enhanced performance in heterogeneous catalysis. Finally, the prospects of MNP/MOF composites in catalysis and remaining issues in this field have been indicated.