PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures

PDB-Ligand (http://www.idrtech.com/PDB-Ligand/) is a three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). It is also a database tool that allows one to browse, classify, superimpose and visualize these structures. As of May 2004, there are about 4870 types of small molecular ligands, experimentally determined as a complex with protein or DNA in the PDB. The proteins that a given ligand binds are often homologous and present the same binding structure to the ligand. However, there are also many instances wherein a given ligand binds to two or more unrelated proteins, or to the same or homologous protein in different binding environments. PDB-Ligand serves as an interactive structural analysis and clustering tool for all the ligand-binding structures in the PDB. PDB-Ligand also provides an easier way to obtain a number of different structure alignments of many related ligand-binding structures based on a simple and flexible ligand clustering method. PDB-Ligand will be a good resource for both a better interpretation of ligand-binding structures and the development of better scoring functions to be used in many drug discovery applications

Fast Scalable Peer-to-Peer Lookup Services for Multi-Hop Wireless Networks

Recent years have seen growing popularity of multi-hop wireless networks such as wireless mesh networks and sensor networks. Such systems require efficient lookup services for reliable system operation such as packet routing, key-discovery, and object lookup. The lack of infrastructure, however, makes the centralized lookup fail to scale in multi-hop wireless networks. For example, consider a citywide wireless mesh network which provides wireless connection service to a number of mobile users. Due to a high volume of user access and inherent vulnerability of wireless links, centralized authentication methods fail to scale. The decentralization of user authentication, however, faces a challenge of key discovery ; how to find the location of user keys. Motivated from the user authentication problem in wireless mesh networks, this dissertation work aims to provide efficient and scalable distributed lookup services for multi-hop wireless networks. Employing the notion of peer-to-peer lookup where each node can both query and respond, I present two different methods: Valley-Walk and Rigs. A loosely-structured scheme Valley-Walk strategically places object copies and locates them efficiently only with a minimal local structure. The Valley-Walk finds target objects in near-optimal hop counts with a moderate number of copies (e.g., 10% the network size) stored in the network. Without a global structure, however, Valley-Walk fails to guarantee the low cost search with a small number of copies. A tightly-structured scheme Rigs (Ring Interval Graph Search) realizes a Distributed Hash Table (DHT) in multi-hop wireless networks. Experimental study shows the limitations of existing DHTs in mult-hop wireless networks due to its independence of underlying topology. Unlike DHT, Rigs constructs a search structure Ring Interval Graph such that queries are forwarded only to local neighbors. Rigs guarantees successful object lookup with near-optimal performance

Double resonance of Raman transitions in a degenerate Fermi gas

We measure momentum-resolved Raman spectra of a spin-polarized degenerate Fermi gas of $^{173}$Yb atoms for a wide range of magnetic fields, where the atoms are irradiated by a pair of counterpropagating Raman laser beams as in the conventional spin-orbit coupling scheme. Double resonance of first- and second-order Raman transitions occurs at a certain magnetic field and the spectrum exhibits a doublet splitting for high laser intensities. The measured spectral splitting is quantitatively accounted for by the Autler-Townes effect. We show that our measurement results are consistent with the spinful band structure of a Fermi gas in the spatially oscillating effective magnetic field generated by the Raman laser fields.Comment: 7 pages, 6 figure

Electrical Investigation of the Oblique Hanle Effect in Ferromagnet/Oxide/Semiconductor Contacts

We have investigated the electrical Hanle effect with magnetic fields applied at an oblique angle ({\theta}) to the spin direction (the oblique Hanle effect, OHE) in CoFe/MgO/semiconductor (SC) contacts by employing a three-terminal measurement scheme. The electrical oblique Hanle signals obtained in CoFe/MgO/Si and CoFe/MgO/Ge contacts show clearly different line shapes depending on the spin lifetime of the host SC. Notably, at moderate magnetic fields, the asymptotic values of the oblique Hanle signals (in both contacts) are consistently reduced by a factor of cos^2({\theta}) irrespective of the bias current and temperature. These results are in good agreement with predictions of the spin precession and relaxation model for the electrical oblique Hanle effect. At high magnetic fields where the magnetization of CoFe is significantly tilted from the film plane to the magnetic field direction, we find that the observed angular dependence of voltage signals in the CoFe/MgO/Si and CoFe/MgO/Ge contacts are well explained by the OHE, considering the misalignment angle between the external magnetic field and the magnetization of CoFe.Comment: 19 pages, 8 figure

Delayed presentation of cerebellar and spinal cord infarction as a complication of computed tomography-guided transthoracic lung biopsy: a case report

INTRODUCTION: Computed tomography-guided transthoracic needle biopsy is a common diagnostic procedure that is associated with various complications including pneumothorax, parenchymal hemorrhage, and hemoptysis. A systemic air embolism is a very rare (0.06 to 0.21%) but potentially fatal complication. CASE PRESENTATION: A 70-year-old Korean male was admitted to our hospital for evaluation of a solitary pulmonary nodule located adjacent to the right inferior pulmonary vein in the medial basal segment of the right lower lobe. A computed tomography-guided needle biopsy was performed by a radiologist using a coaxial needle. A computed tomography image obtained immediately after the biopsy showed intraluminal free air in the proximal ascending aorta. He complained of a mild electrical current sensation in both lower extremities. After three hours he complained of neurological deficit in both lower extremities as well as voiding difficulty. The brain and spine magnetic resonance images showed a right cerebellar and spinal cord infarction at the T8-10 levels. CONCLUSIONS: We report a case of air embolism to the cerebellum and spinal cord causing infarction presenting with an initial symptom of mild electrical current sensation in both lower extremities during the transthoracic needle biopsy. For this potentially fatal complication, early recognition, followed by prompt therapy is critical to reducing morbidity and mortality

Ultraviolet photodepletion spectroscopy of dibenzo-18-crown-6-ether complexes with alkali metal cations

Ultraviolet photodepletion spectra of dibenzo-18-crown-6-ether complexes with alkali metal cations (M+-DB18C6, M = Cs, Rb, K, Na, and Li) were obtained in the gas phase using electrospray ionization quadrupole ion-trap reflectron time-of-flight mass spectrometry. The spectra exhibited a few distinct absorption bands in the wavenumber region of 35450−37800 cm^(−1). The lowest-energy band was tentatively assigned to be the origin of the S_0-S_1 transition, and the second band to a vibronic transition arising from the “benzene breathing” mode in conjunction with symmetric or asymmetric stretching vibration of the bonds between the metal cation and the oxygen atoms in DB18C6. The red shifts of the origin bands were observed in the spectra as the size of the metal cation in M^+-DB18C6 increased from Li^+ to Cs^+. We suggested that these red shifts arose mainly from the decrease in the binding energies of larger-sized metal cations to DB18C6 at the electronic ground state. These size effects of the metal cations on the geometric and electronic structures, and the binding properties of the complexes at the S_0 and S_1 states were further elucidated by theoretical calculations using density functional and time-dependent density functional theories

Triflumizole

In the title compound {systematic name: 4-chloro-N-[1-(1H-imidazol-1-yl)-2-propoxyethyl­idene]-2-(trifluoro­meth­yl)aniline}, C15H15ClF3N3O, the dihedral angle between the aniline and imidazole ring planes is 81.80 (4)°. In the crystal structure, weak inter­molecular C—H⋯X (X = N, O or F) hydrogen bonds and C—H⋯π inter­actions help to consolidate the packing