Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases

Hyperlink Management System (HMS) is a system for automatically updating and maintaining hyperlinks among major public databases in the field of life science. We daily create corresponding tables of data IDs of major databases for human genes and proteins, and provide a CGI-program that returns correct and up-to-date URLs for showing data of various databases that correspond to user-specified IDs. The HMS can deal with various IDs: accession numbers of International Nucleotide Sequence Databases, HUGO Gene Symbols and IDs of UniProt, PDB, H-InvDB and others, and it can return URLs of various databases: H-InvDB, HUGO Gene Nomenclature Committee Database, NCBI Entrez Gene, UniProt, PDB and others. For example, 23 297 pages of Locus view of H-InvDB are reachable by using HUGO Gene Symbols through the HMS. Not only the CGI-program, the HMS provides a Web page for finding and opening URLs of these databases. Although hyperlinking is an effective way of relating biological data among different databases, updating hyperlinks has been a laborious work. The HMS fully automates the job, enabling maintenance-free hyperlinks. We also developed the ID Converter System (ICS) for simply converting data IDs by using corresponding tables in the HMS. The HMS and ICS are freely available at http://biodb.jp/

Flare Ribbons Observed with G-band and FeI 6302A Filters of the Solar Optical Telescope on Board Hinode

The Solar Optical Telescope (SOT) on board Hinode satellite observed an X3.4 class flare on 2006 December 13. Typical two-ribbon structure was observed, not only in the chromospheric CaII H line but also in G-band and FeI 6302A line. The high-resolution, seeing-free images achieved by SOT revealed, for the first time, the sub-arcsec fine structures of the "white light" flare. The G-band flare ribbons on sunspot umbrae showed a sharp leading edge followed by a diffuse inside, as well as previously known core-halo structure. The underlying structures such as umbral dots, penumbral filaments and granules were visible in the flare ribbons. Assuming that the sharp leading edge was directly heated by particle beam and the diffuse parts were heated by radiative back-warming, we estimate the depth of the diffuse flare emission using the intensity profile of the flare ribbon. We found that the depth of the diffuse emission is about 100 km or less from the height of the source of radiative back-warming. The flare ribbons were also visible in the Stokes-V images of FeI 6302A, as a transient polarity reversal. This is probably related to "magnetic transient" reported in the literature. The intensity increase in Stokes-I images indicates that the FeI 6302A line was significantly deformed by the flare, which may cause such a magnetic transient.Comment: 14 pages, 7 figures, PASJ in pres

Benefits of Artificially Generated Gravity Gradients for Interferometric Gravitational-Wave Detectors

We present an approach to experimentally evaluate gravity gradient noise, a potentially limiting noise source in advanced interferometric gravitational wave (GW) detectors. In addition, the method can be used to provide sub-percent calibration in phase and amplitude of modern interferometric GW detectors. Knowledge of calibration to such certainties shall enhance the scientific output of the instruments in case of an eventual detection of GWs. The method relies on a rotating symmetrical two-body mass, a Dynamic gravity Field Generator (DFG). The placement of the DFG in the proximity of one of the interferometer's suspended test masses generates a change in the local gravitational field detectable with current interferometric GW detectors.Comment: 16 pages, 4 figure

Statistics of low-energy levels of a one-dimensional weakly localized Frenkel exciton: A numerical study

Numerical study of the one-dimensional Frenkel Hamiltonian with on-site randomness is carried out. We focus on the statistics of the energy levels near the lower exciton band edge, i. e. those determining optical response. We found that the distribution of the energy spacing between the states that are well localized at the same segment is characterized by non-zero mean, i.e. these states undergo repulsion. This repulsion results in a local discrete energy structure of a localized Frenkel exciton. On the contrary, the energy spacing distribution for weakly overlapping local ground states (the states with no nodes within their localization segments) that are localized at different segments has zero mean and shows almost no repulsion. The typical width of the latter distribution is of the same order as the typical spacing in the local discrete energy structure, so that this local structure is hidden; it does not reveal itself neither in the density of states nor in the linear absorption spectra. However, this structure affects the two-exciton transitions involving the states of the same segment and can be observed by the pump-probe spectroscopy. We analyze also the disorder degree scaling of the first and second momenta of the distributions.Comment: 10 pages, 6 figure

Magnetic Reconnection in Non-Equilibrium Ionization Plasma

We have studied the effect of time-dependent ionization and recombination processes on magnetic reconnection in the solar corona. Petschek-type steady reconnection, in which model the magnetic energy is mainly converted at the slow-mode shocks, was assumed. We carried out the time-dependent ionization calculation in the magnetic reconnection structure. We only calculated the transient ionization of iron; the other species were assumed to be in ionization equilibrium. The intensity of line emissions at specific wavelengths were also calculated for comparison with {\it Hinode} or other observations in future. What we found is as follows: (1) iron is mostly in non-equilibrium ionization in the reconnection region, (2) the intensity of line emission estimated by the time-dependent ionization calculation is significantly different from that with the ionization equilibrium assumption, (3) the effect of time-dependent ionization is sensitive to the electron density in the case that the electron density is less than $10^{10}$ cm$^{-3}$, (4) the effect of thermal conduction lessens the time-dependent ionization effect, (5) the effect of radiative cooling is negligibly small even if we take into account time-dependent ionization.Comment: accepted for publication in The Astrophysical Journa

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Mechanisms underlying fatigue: a voxel-based morphometric study of chronic fatigue syndrome

BACKGROUND: Fatigue is a crucial sensation that triggers rest, yet its underlying neuronal mechanisms remain unclear. Intense long-term fatigue is a symptom of chronic fatigue syndrome, which is used as a model to study the mechanisms underlying fatigue. METHODS: Using magnetic resonance imaging, we conducted voxel-based morphometry of 16 patients and 49 age-matched healthy control subjects. RESULTS: We found that patients with chronic fatigue syndrome had reduced gray-matter volume in the bilateral prefrontal cortex. Within these areas, the volume reduction in the right prefrontal cortex paralleled the severity of the fatigue of the subjects. CONCLUSION: These results are consistent with previous reports of an abnormal distribution of acetyl-L-carnitine uptake, which is one of the biochemical markers of chronic fatigue syndrome, in the prefrontal cortex. Thus, the prefrontal cortex might be an important element of the neural system that regulates sensations of fatigue

Amyloid-PET and 18F-FDG-PET in the diagnostic investigation of Alzheimer's disease and other dementias

Various biomarkers are available to support the diagnosis of neurodegenerative diseases in clinical and research settings. Among the molecular imaging biomarkers, amyloid-PET, which assesses brain amyloid deposition, and 18F-fluorodeoxyglucose (18F-FDG) PET, which assesses glucose metabolism, provide valuable and complementary information. However, uncertainty remains regarding the optimal timepoint, combination, and an order in which these PET biomarkers should be used in diagnostic evaluations because conclusive evidence is missing. Following an expert panel discussion, we reached an agreement on the specific use of the individual biomarkers, based on available evidence and clinical expertise. We propose a diagnostic algorithm with optimal timepoints for these PET biomarkers, also taking into account evidence from other biomarkers, for early and differential diagnosis of neurodegenerative diseases that can lead to dementia. We propose three main diagnostic pathways with distinct biomarker sequences, in which amyloid-PET and 18F-FDG-PET are placed at different positions in the order of diagnostic evaluations, depending on clinical presentation. We hope that this algorithm can support diagnostic decision making in specialist clinical settings with access to these biomarkers and might stimulate further research towards optimal diagnostic strategies