Synthesis and structural characterization of thin multi-walled carbon nanotubes with a partially facetted cross section by a floating reactant method

ArticleCarbon. 43(11):2243-2250 (2005)journal articl

Preparation of Fe-Pt thin-sheet magnets using exfoliation behavior

In this research, Fe-Pt thin sheets thicker than 10 microns with Fe contents ranging from 50 to 60 at.% were prepared. Isotropic Fe-Pt thin sheets could be obtained by taking advantage of the exfoliation behavior after depositing Fe-Pt films on Si substrates using a laser ablation technique. A post-annealing process was used to obtain the L10 phase, and the (BH)max value of Fe-Pt thin sheets showed approximately 70 kJ/m3. Moreover, the test of a cantilever containing the obtained Fe-Pt thin sheet showed good mechanical characteristics

PPLook: an automated data mining tool for protein-protein interaction

<p>Abstract</p> <p>Background</p> <p>Extracting and visualizing of protein-protein interaction (PPI) from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of tools to extract PPI, visualize and classify the results.</p> <p>Results</p> <p>We developed a PPI search system, termed PPLook, which automatically extracts and visualizes protein-protein interaction (PPI) from text. Given a query protein name, PPLook can search a dataset for other proteins interacting with it by using a keywords dictionary pattern-matching algorithm, and display the topological parameters, such as the number of nodes, edges, and connected components. The visualization component of PPLook enables us to view the interaction relationship among the proteins in a three-dimensional space based on the OpenGL graphics interface technology. PPLook can also provide the functions of selecting protein semantic class, counting the number of semantic class proteins which interact with query protein, counting the literature number of articles appearing the interaction relationship about the query protein. Moreover, PPLook provides heterogeneous search and a user-friendly graphical interface.</p> <p>Conclusions</p> <p>PPLook is an effective tool for biologists and biosystem developers who need to access PPI information from the literature. PPLook is freely available for non-commercial users at <url>http://meta.usc.edu/softs/PPLook</url>.</p

Predictability study on the aftershock sequence following the 2011 Tohoku-Oki, Japan, earthquake: first results

Although no deterministic and reliable earthquake precursor is known to date, we are steadily gaining insight into probabilistic forecasting that draws on space–time characteristics of earthquake clustering. Clustering-based models aiming to forecast earthquakes within the next 24 hours are under test in the global project ‘Collaboratory for the Study of Earthquake Predictability’ (CSEP). The 2011 March 11 magnitude 9.0 Tohoku-Oki earthquake in Japan provides a unique opportunity to test the existing 1-day CSEP models against its unprecedentedly active aftershock sequence. The original CSEP experiment performs tests after the catalogue is finalized to avoid bias due to poor data quality. However, this study differs from this tradition and uses the preliminary catalogue revised and updated by the Japan Meteorological Agency (JMA), which is often incomplete but is immediately available. This study is intended as a first step towards operability-oriented earthquake forecasting in Japan. Encouragingly, at least one model passed the test in most combinations of the target day and the testing method, although the models could not take account of the megaquake in advance and the catalogue used for forecast generation was incomplete. However, it can also be seen that all models have only limited forecasting power for the period immediately after the quake. Our conclusion does not change when the preliminary JMAcatalogue is replaced by the finalized one, implying that the models perform stably over the catalogue replacement and are applicable to operational earthquake forecasting. However, we emphasize the need of further research on model improvement to assure the reliability of forecasts for the days immediately after the main quake. Seismicity is expected to remain high in all parts of Japan over the coming years. Our results present a way to answer the urgent need to promote research on time-dependent earthquake predictability to prepare for subsequent large earthquakes in the near future in Japan.Published653-6583.1. Fisica dei terremotiJCR Journalrestricte

Text Mining the History of Medicine

Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform

An EST-SSR Linkage Map of Raphanus sativus and Comparative Genomics of the Brassicaceae†

Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at http://marker.kazusa.or.jp/Daikon

Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry

Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain), OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM) and pattern recognition based classifiers). Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER) accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR