PiSite: a database of protein interaction sites using multiple binding states in the PDB

The vast accumulation of protein structural data has now facilitated the observation of many different complexes in the PDB for the same protein. Therefore, a single protein complex is not sufficient to identify their interaction sites, especially for proteins with multiple binding states or different partners, such as hub proteins. PiSite is a database that provides protein–protein interaction sites at the residue level with consideration of multiple complexes at the same time, by mapping the binding sites of all complexes containing the same protein in the PDB. PiSite provides easy web interfaces with an interactive viewer working with typical web browsers, and the different binding modes can be checked visually. All of the information can also be downloaded for further analyses. In addition, PiSite provides a list of proteins with multiple binding partners and multiple binding states, as well as up-to-date statistics of protein–protein interfaces. PiSite is available at http://pisite.hgc.j

Rotational dynamics of optically trapped polymeric nanofibers

The optical trapping of polymeric nanofibers and the characterization of the rotational dynamics are reported. A strategy to apply a torque to a polymer nanofiber, by tilting the trapped fibers using a symmetrical linear polarized Gaussian beam is demonstrated. Rotation frequencies up to 10 Hz are measured, depending on the trapping power, the fiber length and the tilt angle. A comparison of the experimental rotation frequencies in the different trapping configurations with calculations based on optical trapping and rotation of linear nanostructures through a T-Matrix formalism, accurately reproduce the measured data, providing a comprehensive description of the trapping and rotation dynamics.Comment: (21 pages, 5 figures

Gastric Varices with Remarkable Collateral Veins in Valpronic Acid-Induced Chronic Pancreatitis

Valproic acid (VPA) is a commonly prescribed and approved treatment for epilepsy, including Angelman syndrome, throughout the world. However, the long-term administration of drugs like VPA is associated with the possible development of gastric varices and splenic obstruction as a result of chronic pancreatitis. Such cases can be difficult to treat using endoscopy or interventional radiology because of hemodynamic abnormalities; therefore, surgical treatment is often necessary

Electronic transport in strongly anisotropic disordered systems: model for the random matrix theory with non-integer beta

We study numerically an electronic transport in strongly anisotropic weakly disorderd two-dimensional systems. We find that the conductance distribution is gaussian but the conductance fluctuations increase when anisotropy becomes stronger. We interpret this result by random matrix theory with non-integer symmetry parameter beta, in accordance with recent theoretical work of K.A.Muttalib and J.R.Klauder [Phys.Rev.Lett. 82 (1999) 4272]. Analysis of the statistics of transport paramateres supports this hypothesis.Comment: 8 pages, 7 *.eps figure

Conductance fluctuations and boundary conditions

The conductance fluctuations for various types for two-- and three--dimensional disordered systems with hard wall and periodic boundary conditions are studied, all the way from the ballistic (metallic) regime to the localized regime. It is shown that the universal conductance fluctuations (UCF) depend on the boundary conditions. The same holds for the metal to insulator transition. The conditions for observing the UCF are also given.Comment: 4 pages RevTeX, 5 figures include

Interplay between Coulomb Blockade and Resonant Tunneling studied by the Keldysh Green's Function Method

A theory of tunneling through a quantum dot is presented which enables us to study combined effects of Coulomb blockade and discrete energy spectrum of the dot. The expression of tunneling current is derived from the Keldysh Green's function method, and is shown to automatically satisfy the conservation at DC current of both junctions.Comment: 4 pages, 3 figures(mail if you need), use revtex.sty, error corrected, changed titl

Multiple myeloma presenting as an intracranial plasmacytoma: a case report

Multiple myeloma presenting as an intracranial tumor (plasmacytoma) is very rare. An 81-year-old woman was admitted to our hospital because of gait disturbance. A blood laboratory test revealed a mildly increased lactate dehydrogenase (236 IU/L) and glucose (121 mg/dl). Blood protein fractions were normal. Brain computed tomography and magnetic resonance imaging revealed an intracranial mass (5 × 4 × 3 cm) in the brain base next to the clavus, and it was clinically diagnosed as chordoma. An excision of the brain tumor was performed. Imaging modalities including ultrasound, x-ray, computed tomography, magnetic resonance imaging and positron emission tomography did not reveal any tumors other than the brain tumor. The tumor was soft, fragile, and bloody. Microscopically, a monotonous proliferation of atypical plasma cells with hyperchromatic nuclei was recognized. Histochemically, the tumor cells were pyroninophilic and the congo-red stain revealed amyloidosis. Immunohistochemically, the tumor cells were positive for κ-chain and negative for cytokeratin, epithelial membrane antigen, vimentin, CD45, CD20, CD45RO, λ-chain, IgM, IgA, IgG, synaptophysin, chromogranin, S100 protein, desmin, α-smooth muscle antigen, myoglobin, p53 protein, and glial fibrillary acidic protein. The Ki-67 labeling was 11%. Intracranial plasmacytoma was pathologically diagnosed. The patient was treated by adjuvant chemoradiation, and entered into the complete remission stage. However, multiple metastases emerged in the vertebral bones and ribs six months after the remission. A diagnosis of multiple myeloma was made. The urine revealed Bence-Jones protein of monoclonal IgG κ-chain type, but blood M protein was not recognized. The patient's condition gradually deteriorated. The patient died of respiratory failure due to bronchopneumonia 18 months after the admission. The present case indicates that multiple myeloma may manifest as an intracranial brain tumor (plasmacytoma)

Global 3-D distribution of aerosol composition by synergistic use of CALIOP and MODIS observations

For the observation of the global three-dimensional distribution of aerosol composition and the evaluation of the shortwave direct radiative effect (SDRE) by aerosols, we developed a retrieval algorithm that uses observation data from the Cloud–Aerosol Lidar with Orthogonal Polarization (CALIOP) on board the Cloud–Aerosol Lidar Infrared Pathfinder Satellite Observations (CALIPSO) satellite and the Moderate Resolution Imaging Spectroradiometer (MODIS) on board Aqua. The CALIOP–MODIS retrieval optimizes the aerosol composition to both the CALIOP and MODIS observations in the daytime. Aerosols were assumed to be composed of four aerosol components: water-soluble (WS), light-absorbing (LA), dust (DS), and sea salt (SS) particles. The outputs of the CALIOP–MODIS retrieval are the vertical profiles of the extinction coefficient (αa), single-scattering albedo (ω0), asymmetry factor (g) of total aerosols (WS+LA+DS+SS), and αa of WS, LA, DS, and SS. Daytime observations of CALIOP and MODIS in 2010 were analyzed by the CALIOP–MODIS retrieval. The global means of the aerosol optical depth (τa) at 532 nm were 0.147±0.148 for total aerosols, 0.072±0.085 for WS, 0.027±0.035 for LA, 0.025±0.054 for DS, and 0.023±0.020 for SS. τa of the CALIOP–MODIS retrieval was between those of the CALIPSO and MODIS standard products and was close to the MODIS standard product. The global means of ω0 and g were 0.940±0.038 and 0.718±0.037; these values are in the range of those reported by previous studies. The horizontal distribution of each aerosol component was reasonable; for example, DS was large in desert regions, and LA was large in the major regions of biomass burning and anthropogenic aerosol emissions. The values of τa, ω0, g, and fine and coarse median radii of the CALIOP–MODIS retrieval were compared with those of the AERONET products. τa at 532 and 1064 nm of the CALIOP–MODIS retrieval agreed well with the AERONET products. The ω0, g, and fine and coarse median radii of the CALIOP–MODIS retrieval were not far from those of the AERONET products, but the variations were large, and the coefficients of determination for linear regression between them were small. In the retrieval results for 2010, the clear-sky SDRE values for total aerosols at the top and bottom of the atmosphere were -4.99±3.42 and -13.10±9.93 W m−2, respectively, and the impact of total aerosols on the heating rate was from 0.0 to 0.5 K d−1. These results are generally similar to those of previous studies, but the SDRE at the bottom of the atmosphere is larger than that reported previously. Consequently, comparison with previous studies showed that the CALIOP–MODIS retrieval results were reasonable with respect to aerosol composition, optical properties, and the SDRE.</p

The Phyre2 web portal for protein modeling, prediction and analysis

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission