Mtric from Non-Metric Action of Gravity

The action of general relativity proposed by Capovilla, Jacobson and Dell is written in terms of $SO(3)$ gauge fields and gives Ashtekar's constraints for Einstein gravity. However, it does not depend on the space-time metric nor its signature explicitly. We discuss how the space-time metric is introduced from algebraic relations of the constraints and the Hamiltonian by focusing our attention on the signature factor. The system describes both Euclidian and Lorentzian metrics depending on reality assignments of the gauge connections. That is, Euclidian metrics arise from the real gauge fields. On the other hand, self-duality of the gauge fields, which is well known in the Ashtekar's formalism, is also derived in this theory from consistency condition of Lorentzian metric. We also show that the metric so determined is equivalent to that given by Urbantke, which is usually accepted as a definition of the metric for this system.Comment: 9

In vivo volumetric imaging of human retinal circulation with phase-variance optical coherence tomography

We present in vivo volumetric images of human retinal micro-circulation using Fourier-domain optical coherence tomography (Fd-OCT) with the phase-variance based motion contrast method. Currently fundus fluorescein angiography (FA) is the standard technique in clinical settings for visualizing blood circulation of the retina. High contrast imaging of retinal vasculature is achieved by injection of a fluorescein dye into the systemic circulation. We previously reported phase-variance optical coherence tomography (pvOCT) as an alternative and non-invasive technique to image human retinal capillaries. In contrast to FA, pvOCT allows not only noninvasive visualization of a two-dimensional retinal perfusion map but also volumetric morphology of retinal microvasculature with high sensitivity. In this paper we report high-speed acquisition at 125 kHz A-scans with pvOCT to reduce motion artifacts and increase the scanning area when compared with previous reports. Two scanning schemes with different sampling densities and scanning areas are evaluated to find optimal parameters for high acquisition speed in vivo imaging. In order to evaluate this technique, we compare pvOCT capillary imaging at 3x3 mm^2 and 1.5x1.5 mm^2 with fundus FA for a normal human subject. Additionally, a volumetric view of retinal capillaries and a stitched image acquired with ten 3x3 mm^2 pvOCT sub-volumes are presented. Visualization of retinal vasculature with pvOCT has potential for diagnosis of retinal vascular diseases

Logical Operation Based Literature Association with Genes and its application, PosMed.

PosMed prioritizes candidate genes for positional cloning by employing our original database search engine GRASE, which uses an inferential process similar to an artificial neural network comprising documental neurons (or 'documentrons') that represent each document contained in databases such as MEDLINE and OMIM (Yoshida, _et al_. 2009, Makita, _et al_. 2009). PosMed immediately ranks the candidate genes by connecting phenotypic keywords to the genes through connections representing gene–gene interactions other biological relationships, such as metabolite–gene, mutant mouse–gene, drug–gene, disease–gene, and protein–protein interactions, ortholog data, and gene–literature connections.

To make proper relationships between genes and literature, we manually curate queries, which are defined by logical operation rules, against MEDLINE. For example, to detect a set of MEDLINE documents for the AT1G03880 gene in _A. thaliana_, we applied the following logical query: (‘AT1G03880’ OR ‘CRU2’ OR ‘CRB’ OR ‘CRUCIFERIN 2' OR ‘CRUCIFERIN B’) AND (‘Arabidopsis’) NOT (‘chloroplast RNA binding’). Curators refined these queries in mouse, rice and _A. thaliana_. For human and rat genes, we use mouse curation results via ortholog genes in PosMed.

PosMed is available at "http://omicspace.riken.jp/PosMed":http://omicspace.riken.jp/PosMed

References:
Yoshida Y, et al. _Nucleic Acids Res_. 37(Web Server issue):W147-52. 2009. 
Makita Y, et al. _Plant Cell Physiol_. 2009 Jul;50(7):1249-59.
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A Movie Genre Prediction Based on Multi-Variate Bernoulli Model and Genre Correlations

In this paper, a movie category based on Bayesian model and categories correlations is proposed. Although several methods have been reported on improving the user satisfaction based on unexpectedness metric, to the best of our knowledge, predicting items’ categories rather than predicting items’ rating is a new attempt. This in turn completes the items’ categories given by experts and improves user satisfaction by providing a surprise effect in the recommendations given to users. We employ Bernoulli multivariate model to estimate a likelihood of a movie given category and the Bayes rule to evaluate the posterior probability of a genre given a movie. Experiments with the MovieLens dataset validate our approach

Beam Induced Electron Cloud Resonances in Dipole Magnetic Fields

The buildup of low energy electrons in an accelerator, known as electron cloud, can be severely detrimental to machine performance. Under certain beam conditions, the beam can become resonant with the cloud dynamics, accelerating the buildup of electrons. This paper will examine two such effects: multipacting resonances, in which the cloud development time is resonant with the bunch spacing, and cyclotron resonances, in which the cyclotron period of electrons in a magnetic field is a multiple of bunch spacing. Both resonances have been studied directly in dipole fields using retarding field analyzers installed in the Cornell Electron Storage Ring (CESR). These measurements are supported by both analytical models and computer simulations

The risk of rabies spread in Japan: a mathematical modeling assessment

Rabies was eliminated from Japan in 1957. In the 60 years since elimination, vaccination coverage has declined and dog ownership habits have changed. The purpose of this study was to assess the current risk of rabies spread in Japan. A spatially explicit transmission model was developed at the 1 km2 grid scale for Hokkaido and Ibaraki Prefectures. Parameters associated with dog movement and bite injuries were estimated using historical records from Japan, and were used with previously published epidemiological parameters. The final epidemic size, efficacy of rabies contingency plans and the influence of dog owner responses to incursions were assessed by the model. Average outbreak sizes for dog rabies were 3.1 and 4.7 dogs in Hokkaido and Ibaraki Prefectures, respectively. Average number of bite injury cases were 4.4 and 6.7 persons in Hokkaido and Ibaraki Prefectures, respectively. Discontinuation of mandatory vaccination increased outbreak sizes in these prefectures. Sensitivity analyses showed that higher chance of unintentional release of rabid dogs by their owners (from 0.5 to 0.9 probability) increased outbreak size twofolds. Our model outputs suggested that at present, incursions of rabies into Japan are very unlikely to cause large outbreaks. Critically, the reaction of dog owners to their dogs developing rabies considerably impacts the course of outbreaks. Contingency measures should therefore include sensitisation of dog owners

Bioenergetics in Photosystem I: Time-Resolved Step-Scan FTIR and Visible Spectroscopic Studies of the Secondary Electron Acceptor A1

Time-resolved infrared and visible absorption difference spectroscopy was applied for the study of electron transfer (ET) reactions involving A1, the secondary electron acceptor in photosystem I (PSI). In PSI, the secondary electron acceptor A1 is a phylloquinone (PhQ) molecule. Flash-induced absorption changes at room and cryogenic temperatures in the infrared and visible spectral ranges were probed for PSI with a series of native and non-native quinones in the A1 binding site. Obtained kinetic and spectral data were analyzed for the functional and structural properties of A1 and PSI. Using transient absorption spectroscopy in the visible spectral range, the rates and directionality of ET processes in PSI with modified A1 were determined. A detailed kinetic simulation model was constructed and solved in the context of Marcus ET theory, and midpoint redox potentials of A1 was predicted within a tight range. The transient absorption kinetics for ten different quinones and the kinetic simulation revealed that the wasteful charge recombination process in native PSI occurs in the inverted region. Although inverted-region ET had been widely suggested to be an important mechanism contributing to photosynthetic efficiency, the mechanism had never been demonstrated in any native photosynthetic system. The result presented here is the first demonstration of inverted-region ET in a native photosynthetic reaction center in physiological conditions. Through Marcus theory-based simulation, inverted-region ET is quantitatively shown to be an important mechanism underlying the high efficiency in PSI ET. Time-resolved infrared difference spectroscopy was undertaken using step-scan FTIR technique with a microsecond temporal resolution. Highly-resolved double difference spectrum was constructed to identify infrared bands due to PhQ in the A1 binding site. Assisted by the DFT-based vibrational frequency calculations, vibrational modes due to anionic PhQ– were identified. The calculations suggest that PhQ is asymmetrically H-bonded, and that this interaction is especially strong for PhQ–, but not for PhQ. Additionally, discrepancies that previously existed between FTIR and EPR studies on PSI with plastoquinone-9 in the A1 site were resolved. A method to incorporate a benzoquinone was established, and (A1– – A1) FTIR difference spectra for a series of benzoquinones were produced for the first time