Dry mantle transition zone inferred from the conductivity of wadsleyite and ringwoodite.

The Earth's mantle transition zone could potentially store a large amount of water, as the minerals wadsleyite and ringwoodite incorporate a significant amount of water in their crystal structure. The water content in the transition zone can be estimated from the electrical conductivities of hydrous wadsleyite and ringwoodite, although such estimates depend on accurate knowledge of the two conduction mechanisms in these minerals (small polaron and proton conductions), which early studies have failed to distinguish between. Here we report the electrical conductivity of these two minerals obtained by high-pressure multi-anvil experiments. We found that the small polaron conductions of these minerals are substantially lower than previously estimated. The contributions of proton conduction are small at temperatures corresponding to the mantle transition zone and the conductivity of wadsleyite is considerably lower than that of ringwoodite for both mechanisms. The dry model mantle shows considerable conductivity jumps associated with the olivine-wadsleyite, wadsleyite-ringwoodite and post-spinel transitions. Such a dry model explains well the currently available conductivity-depth profiles obtained from geoelectromagnetic studies. We therefore conclude that there is no need to introduce a significant amount of water in the mantle transition to satisfy electrical conductivity constraints.

Active joint mechanism driven by multiple actuators made of flexible bags: a proposal of dual structural actuator.

An actuator is required to change its speed and force depending on the situation. Using multiple actuators for one driving axis is one of the possible solutions; however, there is an associated problem of output power matching. This study proposes a new active joint mechanism using multiple actuators. Because the actuator is made of a flexible bag, it does not interfere with other actuators when it is depressurized. The proposed joint achieved coordinated motion of multiple actuators. This report also discusses a new actuator which has dual cylindrical structure. The cylinders are composed of flexible bags with different diameters. The joint torque is estimated based on the following factors: empirical formula for the flexible actuator torque, geometric relationship between the joint and the actuator, and the principle of virtual work. The prototype joint mechanism achieves coordinated motion of multiple actuators for one axis. With this motion, small inner actuator contributes high speed motion, whereas large outer actuator generates high torque. The performance of the prototype joint is examined by speed and torque measurements. The joint showed about 30% efficiency at 2.0 Nm load torque under 0.15 MPa air input.

Improving protein coreference resolution by simple semantic classification.

BACKGROUND: Current research has shown that major difficulties in event extraction for the biomedical domain are traceable to coreference. Therefore, coreference resolution is believed to be useful for improving event extraction. To address coreference resolution in molecular biology literature, the Protein Coreference (COREF) task was arranged in the BioNLP Shared Task (BioNLP-ST, hereafter) 2011, as a supporting task. However, the shared task results indicated that transferring coreference resolution methods developed for other domains to the biological domain was not a straight-forward task, due to the domain differences in the coreference phenomena. RESULTS: We analyzed the contribution of domain-specific information, including the information that indicates the protein type, in a rule-based protein coreference resolution system. In particular, the domain-specific information is encoded into semantic classification modules for which the output is used in different components of the coreference resolution. We compared our system with the top four systems in the BioNLP-ST 2011; surprisingly, we found that the minimal configuration had outperformed the best system in the BioNLP-ST 2011. Analysis of the experimental results revealed that semantic classification, using protein information, has contributed to an increase in performance by 2.3% on the test data, and 4.0% on the development data, in F-score. CONCLUSIONS: The use of domain-specific information in semantic classification is important for effective coreference resolution. Since it is difficult to transfer domain-specific information across different domains, we need to continue seek for methods to utilize such information in coreference resolution.

Hydrous olivine unable to account for conductivity anomaly at the top of the asthenosphere.

The oceanic asthenosphere is observed to have high electrical conductivity, which is highly anisotropic in some locations. In the directions parallel and normal to the plate motion, the conductivity is of the order of 10(-1) and 10(-2) S m(-1), respectively, which cannot be explained by the conductivity of anhydrous olivine. But because hydrogen can be incorporated in olivine at mantle pressures, this observation has been attributed to olivine hydration, which might cause anisotropically high conductivity by proton migration. To examine this hypothesis, here we report the effect of water on electrical conductivity and its anisotropy for hydrogen-doped and undoped olivine at 500-1,500 K and 3 GPa. The hydrous olivine has much higher conductivity and lower activation energy than anhydrous olivine in the investigated temperature range. Nevertheless, extrapolation of the experimental results suggests that conductivity of hydrous olivine at the top of the asthenosphere should be nearly isotropic and only of the order of 10(-2) S m(-1). Our data indicate that the hydration of olivine cannot account for the geophysical observations, which instead may be explained by the presence of partial melt elongated in the direction of plate motion.

PathText: a text mining integrator for biological pathway visualizations.

MOTIVATION: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations.

Voriconazole treatment of pulmonary mycosis caused by Chrysosporium zonatum after treatment for pulmonary tuberculosis.

Chrysosporium zonatum is a soil-dwelling fungus that rarely causes pulmonary infections, and a small number of cases have been reported to date. A 74-year-old man, who had previously been treated for tuberculosis, presented with symptoms of low-grade fever, anorexia, cough, and bloody sputum. Chest computed tomography (CT) showed a thick-walled cavitary lesion in the right upper lobe, in which there was a suspected mycotic mass. Initially, the patient was suspected to have chronic aspergillosis due to positive serum anti-Aspergillus antibodies. However, bronchoscopic culture revealed the growth of C. zonatum. Symptoms and imaging findings improved with administration of voriconazole for 18 months. Infection by C. zonatum is very rare and is difficult to differentiate from aspergillosis by clinical features. Clinicians should be aware of the possibility of coinfection with C. zonatum and Aspergillus sp. Voriconazole may be an effective treatment option.

Evaluating contributions of natural language parsers to protein-protein interaction extraction.

MOTIVATION: While text mining technologies for biomedical research have gained popularity as a way to take advantage of the explosive growth of information in text form in biomedical papers, selecting appropriate natural language processing (NLP) tools is still difficult for researchers who are not familiar with recent advances in NLP. This article provides a comparative evaluation of several state-of-the-art natural language parsers, focusing on the task of extracting protein-protein interaction (PPI) from biomedical papers. We measure how each parser, and its output representation, contributes to accuracy improvement when the parser is used as a component in a PPI system. RESULTS: All the parsers attained improvements in accuracy of PPI extraction. The levels of accuracy obtained with these different parsers vary slightly, while differences in parsing speed are larger. The best accuracy in this work was obtained when we combined Miyao and Tsujii's Enju parser and Charniak and Johnson's reranking parser, and the accuracy is better than the state-of-the-art results on the same data. AVAILABILITY: The PPI extraction system used in this work (AkanePPI) is available online at http://www-tsujii.is.s.u-tokyo.ac.jp/downloads/downloads.cgi. The evaluated parsers are also available online from each developer's site.

New challenges for text mining: mapping between text and manually curated pathways.

BACKGROUND: Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactions, and (3) the formulation and implementation of required inferences based on biological domain knowledge. RESULTS: To address these challenges, we constructed new resources to link the text with a model pathway; they are: the GENIA pathway corpus with event annotation and NF-kB pathway. Through their detailed analysis, we address the untapped resource, 'bio-inference,' as well as the differences between text and pathway representation. Here, we show the precise comparisons of their representations and the nine classes of 'bio-inference' schemes observed in the pathway corpus. CONCLUSIONS: We believe that the creation of such rich resources and their detailed analysis is the significant first step for accelerating the research of the automatic construction of pathway from text.

Pressure dependence of transverse acoustic phonon energy in ferropericlase across the spin transition.

We investigated transverse acoustic (TA) phonons in iron-bearing magnesium oxide (ferropericlase) up to 56 GPa using inelastic x-ray scattering (IXS). The results show that the energy of the TA phonon far from the Brillouin zone center suddenly increases with increasing pressure above the spin transition pressure of ferropericlase. Ab initio calculations revealed that the TA phonon energy far from the Brillouin zone center is higher in the low-spin state than in the high spin state; that the TA phonon energy depend weakly on pressure; and that the energy gap between the TA and the lowest-energy-optic phonons is much narrower in the low-spin state than in the high-spin state. This allows us to conclude that the anomalous behavior of the TA mode in the present experiments is the result of gap narrowing due to the spin transition and explains contradictory results in previous experimental studies.

Discovery of new hydrothermal activity and chemosynthetic fauna on the Central Indian Ridge at 18°-20° S.

Indian Ocean hydrothermal vents are believed to represent a novel biogeographic province, and are host to many novel genera and families of animals, potentially indigenous to Indian Ocean hydrothermal systems. In particular, since its discovery in 2001, much attention has been paid to a so-called 'scaly-foot' gastropod because of its unique iron-sulfide-coated dermal sclerites and the chemosynthetic symbioses in its various tissues. Despite increasing interest in the faunal assemblages at Indian Ocean hydrothermal vents, only two hydrothermal vent fields have been investigated in the Indian Ocean. Here we report two newly discovered hydrothermal vent fields, the Dodo and Solitaire fields, which are located in the Central Indian Ridge (CIR) segments 16 and 15, respectively. Chemosynthetic faunal communities at the Dodo field are emaciated in size and composition. In contrast, at the Solitaire field, we observed faunal communities that potentially contained almost all genera found at CIR hydrothermal environments to date, and even identified previously unreported taxa. Moreover, a new morphotype of 'scaly-foot' gastropod has been found at the Solitaire field. The newly discovered 'scaly-foot' gastropod has similar morphological and anatomical features to the previously reported type that inhabits the Kairei field, and both types of 'scaly-foot' gastropods genetically belong to the same species according to analyses of their COI gene and nuclear SSU rRNA gene sequences. However, the new morphotype completely lacks an iron-sulfide coating on the sclerites, which had been believed to be a novel feature restricted to 'scaly-foot' gastropods. Our new findings at the two newly discovered hydrothermal vent sites provide important insights into the biodiversity and biogeography of vent-endemic ecosystems in the Indian Ocean.

Extracting protein interactions from text with the unified AkaneRE event extraction system.

Currently, relation extraction (RE) and event extraction (EE) are the two main streams of biological information extraction. In 2009, the majority of these RE and EE research efforts were centered around the BioCreative II.5 Protein-Protein Interaction (PPI) challenge and the "BioNLP event extraction shared task." Although these challenges took somewhat different approaches, they share the same ultimate goal of extracting bio-knowledge from the literature. This paper compares the two challenge task definitions, and presents a unified system that was successfully applied in both these and several other PPI extraction task settings. The AkaneRE system has three parts: A core engine for RE, a pool of modules for specific solutions, and a configuration language to adapt the system to different tasks. The core engine is based on machine learning, using either Support Vector Machines or Statistical Classifiers and features extracted from given training data. The specific modules solve tasks like sentence boundary detection, tokenization, stemming, part-of-speech tagging, parsing, named entity recognition, generation of potential relations, generation of machine learning features for each relation, and finally, assignment of confidence scores and ranking of candidate relations. With these components, the AkaneRE system produces state-of-the-art results, and the system is freely available for academic purposes at http://www-tsujii.is.s.u-tokyo.ac.jp/satre/akane/.

Boron-doped diamond heater and its application to large-volume, high-pressure, and high-temperature experiments.

A temperature of 3500 degrees C was generated using a diamond resistance heater in a large-volume Kawai-type high-pressure apparatus. Re and LaCrO(3) have conventionally been used for heaters in high-pressure studies but they cannot generate temperatures higher than 2900 degrees C and make in situ x-ray observations difficult due to their high x-ray absorption. Using a boron-doped diamond heater overcomes these problems and achieves stable temperature generation for pressure over 10 GPa. The heater starting material is a cold-compressed mixture of graphite with boron used to avoid the manufacturing difficulties due to the extreme hardness of diamond. The diamond heater was synthesized in situ from the boron-graphite mixture at temperature of 1600+/-100 degrees C and pressure of 20 GPa. By using the proposed technique, we have employed the diamond heater for high-temperature generation in a large-volume high-pressure apparatus. Achievement of temperatures above 3000 degrees C allows us to measure the melting points of the important constituents in earth's mantle (MgSiO(3), SiO(2), and Al(2)O(3)) and core (Fe and Ni) at extremely high pressures.

Precise determination of elastic constants by high-resolution inelastic X-ray scattering.

Inelastic X-ray scattering (IXS) measurements have been performed on an MgO single crystal in order to evaluate IXS as a methodology for accurate and precise determination of elastic constants and sound velocities. By performing the IXS experiment using a 12-analyzer array, the complete set of single-crystal elastic constants of MgO were determined to a precision better than 0.8% (sound velocities to better than 0.2%). The results are consistent with values in the literature. The precision and accuracy of this work, which is significantly better than other published work to date, demonstrates the potential of IXS in determining elastic properties.