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

Isolation and characterization of resistance gene analogs (RGAs) in sorghum

The largest group of plant disease resistance (R) genes that share similar structures contains a predicted nucleotide-binding site (NBS) domain. NBS domains of this class of R genes show highly conserved amino acid motifs, which makes it possible to isolate resistance gene analogs (RGAs) by PCR with degenerate primers and homology searches from public databases. Multiple combinations of degenerate primers were designed from three conserved motifs (one motif was used for a subgroup-specific primer design) in the NBS regions of R genes of various plants. All combinations of primer pairs were used to amplify genomic DNA from sorghum. TIR-specific primer combinations showed no PCR amplification in sorghum. Homology searches identified many NBS-encoding sequences among the expressed or genomic molecular database entries for sorghum. Motif analysis of the sorghum NBS sequences that were identified in this study revealed eight major conserved motifs plus two additional highly conserved motifs, but no TIR-specific motifs. Phylogenetic analysis of sorghum NBS sequences showed tree topology typical of NBS-LRR genes, including clustered nodes and longbranch lengths. Eleven distinct families of NBS sequences, representing a highly diverse sample, were isolated from Sorghum bicolor. With two exceptions, sorghum RGA families appeared to be closely related in sequence to at least one R-gene cloned from other species. In addition, deduced amino acid sequences of sorghum RGAs showed strong sequence similarity to almost all known non-TIR (Toll/Interleukin 1 Receptor)- type R-genes. Mapping with sorghum RGA markers revealed one linkage group containing four out of ten randomly selected markers, suggesting non-random distribution of NBS sequences in the sorghum genome. Rice sequences homologous to sorghum NBS sequences were found from two-way BLAST searches. Some of them were shown to be orthologs, when determined by using phylogenetic approaches which combined five different evolution models and tree-building methods

The usefulness of the Korean version of modified Mini-Mental State Examination (K-mMMSE) for dementia screening in community dwelling elderly people

BACKGROUND: We assessed whether the Korean version of modified Mini-Mental State Examination (K-mMMSE) has improved performance as a screening test for cognitive impairment or dementia in a general population compared with the Korean Mini-Mental State Examination (K-MMSE). METHODS: Screening interviews were conducted with people aged 65 and over in Noam-dong, Namwon-city, Jeonbuk province. There were 522 community participants, of whom 235 underwent clinical and neuropsychological examination for diagnosis of dementia and Cognitive Impairment No Dementia (CIND). Sensitivity, specificity and areas under the receiver operating characteristic (ROC) curves for the K-mMMSE and the K-MMSE were the main outcome measures. RESULTS: Cronbach's alpha for the K-mMMSE was 0.91, compared with 0.84 for the K-MMSE. The areas under the ROC curves in identifying all levels of CIND or dementia were 0.91 for the K-mMMSE and 0.89 for the K-MMSE (P < 0.05). For the K-mMMSE, the optimal cut-off score for a diagnosis of CIND was 69/70, which had a sensitivity of 0.86 and a specificity of 0.79, while, for a diagnosis of dementia, the optimal cut-off score of 59/60 had a sensitivity of 0.91 and a specificity of 0.78. The K-mMMSE also had a high test-retest reliability (r = 0.89). CONCLUSION: Our findings indicate that the K-mMMSE is more reliable and valid than the K-MMSE as a cognitive screen in a population based study of dementia. Considering the test characteristics, the K-MMSE and modified version are expected to be optimally used in clinical and epidemiologic fields

A study on Biosorptive Removal of Cd from Wastewater using Chironomid Larvae (Diptera: Chironomidae)

Cadmium (Cd) has caused serious public health problem due to its toxic nature. It is necessary to find a cost-effective method to dispose of wastewater containing Cd. Chironomid larvae as an alternative to conventional adsorbents were applied to remove Cd from wastewater. The sorption studies of Cd were carried out using laboratory-reared Glyptotendipes tokunagai (Diptera: Chironomidae) larvae. Kinetic and sorption capacity of chironomid larvae for Cd were determined by means of controlled experiments in a batch system. It was observed that removal efficiency of Cd was largely concentration dependent and more effective in lower concentration. At equilibrium, Cd was removed up to roughly 53 %. The sorption kinetics were found to conform to the pseudo-first-order kinetic model with a good correlation. Equilibrium sorption data were best fitted to the both Freundlich and Langmuir isotherm models owing to their correlation coefficient R2 values greater than 0.99. Considering the values obtained from isotherm constants 1/n and r, it is confirmed that Cd is sorbed favorably by chironomid larvae. With its relatively high removal capability for Cd, Chironomid larvae have enormous potential for application in wastewater treatment technologies.Â

Subcutaneous Sacrococcygeal Myxopapillary Ependymoma in Asian Female:A Case Report

Subcutaneous sacrococcygeal myxopapillary ependymoma is extremely rare tumor that has a tendency to develop in children and adolescents. There have been several case reports and sporadic reports in the literature. However, no case has been reported in an Asian patient, to the best of our knowledge. We describe a 25-year-old Asian female patient with a subcutaneous sacrococcygeal myxopapillary ependymoma that had been clinically diagnosed as a pilonidal cyst. The tumor was treated successfully by surgical excision and the patient is doing well without evidence of local recurrence or distant metastasis at 2 years after surgery.

Boosting thermal conductivity by surface plasmon polaritons propagating along a thin Ti film

We experimentally demonstrate a boosted in-plane thermal conduction by surface plasmon polaritons (SPPs) propagating along a thin Ti film on a glass substrate. Owing to a lossy nature of metal, SPPs can propagate over centimeter-scale distance even with a supported metal film, and resulting ballistic heat conduction can be quantitatively validated. Further, for a 100-nm-thick Ti film on glass substrate, a significant enhancement of in-plane thermal conductivity compared to bulk value ($\sim 35\%$) is experimentally shown. This study will provide a new avenue to employ SPPs for heat dissipation along a supported thin film, which can be readily applied to mitigate hot-spot issues in microelectronics.Comment: 3 figure

Inter-plane artifact suppression in tomosynthesis using 3D CT image data

<p>Abstract</p> <p>Background</p> <p>Despite its superb lateral resolution, flat-panel-detector (FPD) based tomosynthesis suffers from low contrast and inter-plane artifacts caused by incomplete cancellation of the projection components stemming from outside the focal plane. The incomplete cancellation of the projection components, mostly due to the limited scan angle in the conventional tomosynthesis scan geometry, often makes the image contrast too low to differentiate the malignant tissues from the background tissues with confidence.</p> <p>Methods</p> <p>In this paper, we propose a new method to suppress the inter-plane artifacts in FPD-based tomosynthesis. If 3D whole volume CT images are available before the tomosynthesis scan, the CT image data can be incorporated into the tomosynthesis image reconstruction to suppress the inter-plane artifacts, hence, improving the image contrast. In the proposed technique, the projection components stemming from outside the region-of-interest (ROI) are subtracted from the measured tomosynthesis projection data to suppress the inter-plane artifacts. The projection components stemming from outside the ROI are calculated from the 3D whole volume CT images which usually have lower lateral resolution than the tomosynthesis images. The tomosynthesis images are reconstructed from the subtracted projection data which account for the x-ray attenuation through the ROI. After verifying the proposed method by simulation, we have performed both CT scan and tomosynthesis scan on a phantom and a sacrificed rat using a FPD-based micro-CT.</p> <p>Results</p> <p>We have measured contrast-to-noise ratio (CNR) from the tomosynthesis images which is an indicator of the residual inter-plane artifacts on the focal-plane image. In both cases of the simulation and experimental imaging studies of the contrast evaluating phantom, CNRs have been significantly improved by the proposed method. In the rat imaging also, we have observed better visual contrast from the tomosynthesis images reconstructed by the proposed method.</p> <p>Conclusions</p> <p>The proposed tomosynthesis technique can improve image contrast with aids of 3D whole volume CT images. Even though local tomosynthesis needs extra 3D CT scanning, it may find clinical applications in special situations in which extra 3D CT scan is already available or allowed.</p

Micro-nano hybrid structures with manipulated wettability using a two-step silicon etching on a large area

Nanoscale surface manipulation technique to control the surface roughness and the wettability is a challenging field for performance enhancement in boiling heat transfer. In this study, micro-nano hybrid structures (MNHS) with hierarchical geometries that lead to maximizing of surface area, roughness, and wettability are developed for the boiling applications. MNHS structures consist of micropillars or microcavities along with nanowires having the length to diameter ratio of about 100:1. MNHS is fabricated by a two-step silicon etching process, which are dry etching for micropattern and electroless silicon wet etching for nanowire synthesis. The fabrication process is readily capable of producing MNHS covering a wafer-scale area. By controlling the removal of polymeric passivation layers deposited during silicon dry etching (Bosch process), we can control the geometries for the hierarchical structure with or without the thin hydrophobic barriers that affect surface wettability. MNHS without sidewalls exhibit superhydrophilic behavior with a contact angle under 10°, whereas those with sidewalls preserved by the passivation layer display more hydrophobic characteristics with a contact angle near 60°