On Switch-Reference Phenomena in Kolyma Yukaghir

「環太平洋の言語」成果報告書A2-002ELPR publication series A2-00

Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways

BACKGROUND: Interpreting large-scale studies from microarrays or next-generation sequencing for further experimental testing remains one of the major challenges in quantitative biology. Combining expression with physical or genetic interaction data has already been successfully applied to enhance knowledge from all types of high-throughput studies. Yet, toolboxes for navigating and understanding even small gene or protein networks are poorly developed. RESULTS: We introduce two Cytoscape plug-ins, which support the generation and interpretation of experiment-based interaction networks. The virtual pathway explorer viPEr creates so-called focus networks by joining a list of experimentally determined genes with the interactome of a specific organism. viPEr calculates all paths between two or more user-selected nodes, or explores the neighborhood of a single selected node. Numerical values from expression studies assigned to the nodes serve to score identified paths. The pathway enrichment analysis tool PEANuT annotates networks with pathway information from various sources and calculates enriched pathways between a focus and a background network. Using time series expression data of atorvastatin treated primary hepatocytes from six patients, we demonstrate the handling and applicability of viPEr and PEANuT. Based on our investigations using viPEr and PEANuT, we suggest a role of the FoxA1/A2/A3 transcriptional network in the cellular response to atorvastatin treatment. Moreover, we find an enrichment of metabolic and cancer pathways in the Fox transcriptional network and demonstrate a patient-specific reaction to the drug. CONCLUSIONS: The Cytoscape plug-in viPEr integrates –omics data with interactome data. It supports the interpretation and navigation of large-scale datasets by creating focus networks, facilitating mechanistic predictions from –omics studies. PEANuT provides an up-front method to identify underlying biological principles by calculating enriched pathways in focus networks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2017-z) contains supplementary material, which is available to authorized users

Coordination and management of information for construction design projects - a framework for Portugal

In the construction industry in Portugal, the coordination and management of information for construction design projects has been neglected. The use of classification systems and protocols for the communication of information amongst the different stakeholders is poor and inefficient. This research aims to explore the viability of developing a systematic approach to the coordination of information amongst the multiple project stakeholders in the Portuguese Construction Industry. Bearing this in mind, the core research question of this doctoral thesis is: What sort of framework and guidelines are needed for the successful implementation of a classification information system for construction project design data in Portugal, which is accessible to all stakeholders involved? A mixed methods approach was developed for this purpose, with emphasis given to qualitative research techniques. Methods used comprised: literature review, quantitative survey, semi-structured interviews and focus group discussions. Whereas quantitative research methods contributed to a more rigorous interpretation process, qualitative research methods offered a solid description of the former. This methodology was used in order to establish and design a conceptual classification framework model for information coordination and management throughout the design project and construction in Portugal. First, constraints and enablers to framework development and implementation were identified at all levels: political, cultural and behaviour, legal, technical and educational, economic and financial, and organizational issues. Three overarching issues were also identified: corruption, lack of accountability and non-compliance timelines/deadlines. Then, a conceptual framework was developed, detailing 1) content, 2) characteristics of an environment conductive to a successful development, implementation and use of the framework, and 3) guidelines to its dissemination

Magnetic quantum ratchet effect in graphene

A periodically driven system with spatial asymmetry can exhibit a directed motion facilitated by thermal or quantum fluctuations. This so-called ratchet effect has fascinating ramifications in engineering and natural sciences. Graphene is nominally a symmetric system. Driven by a periodic electric field, no directed electric current should flow. However, if the graphene has lost its spatial symmetry due to its substrate or adatoms, an electronic ratchet motion can arise. We report an experimental demonstration of such an electronic ratchet in graphene layers, proving the underlying spatial asymmetry. The orbital asymmetry of the Dirac fermions is induced by an in-plane magnetic field, whereas the periodic driving comes from terahertz radiation. The resulting magnetic quantum ratchet transforms the a.c. power into a d.c. current, extracting work from the out-of-equilibrium electrons driven by undirected periodic forces. The observation of ratchet transport in this purest possible two-dimensional system indicates that the orbital effects may appear and be substantial in other two-dimensional crystals such as boron nitride, molybdenum dichalcogenides and related heterostructures. The measurable orbital effects in the presence of an in-plane magnetic field provide strong evidence for the existence of structure inversion asymmetry in graphene

Mastering the Wrinkling of Self-supported Graphene

Abstract We present an approach that allows for the preparation of well-defined large arrays of graphene wrinkles with predictable geometry. Chemical vapor deposition grown graphene transferred onto hexagonal pillar arrays of SiO2 with sufficiently small interpillar distance forms a complex network of two main types of wrinkle arrangements. The first type is composed of arrays of aligned equidistantly separated parallel wrinkles propagating over large distances, and originates from line interfaces in the graphene, such as thin, long wrinkles and graphene grain boundaries. The second type of wrinkle arrangement is composed of non-aligned short wrinkles, formed in areas without line interfaces. Besides the presented hybrid graphene topography with distinct wrinkle geometries induced by the pre-patterned substrate, the graphene layers are suspended and self-supporting, exhibiting large surface area and negligible doping effects from the substrate. All these properties make this wrinkled graphene a promising candidate for a material with enhanced chemical reactivity useful in nanoelectronic applications