Identification of putative domain linkers by a neural network – application to a large sequence database

BACKGROUND: The reliable dissection of large proteins into structural domains represents an important issue for structural genomics/proteomics projects. To provide a practical approach to this issue, we tested the ability of neural network to identify domain linkers from the SWISSPROT database (101602 sequences). RESULTS: Our search detected 3009 putative domain linkers adjacent to or overlapping with domains, as defined by sequence similarity to either Protein Data Bank (PDB) or Conserved Domain Database (CDD) sequences. Among these putative linkers, 75% were "correctly" located within 20 residues of a domain terminus, and the remaining 25% were found in the middle of a domain, and probably represented failed predictions. Moreover, our neural network predicted 5124 putative domain linkers in structurally un-annotated regions without sequence similarity to PDB or CDD sequences, which suggest to the possible existence of novel structural domains. As a comparison, we performed the same analysis by identifying low-complexity regions (LCR), which are known to encode unstructured polypeptide segments, and observed that the fraction of LCRs that correlate with domain termini is similar to that of domain linkers. However, domain linkers and LCRs appeared to identify different types of domain boundary regions, as only 32% of the putative domain linkers overlapped with LCRs. CONCLUSION: Overall, our study indicates that the two methods detect independent and complementary regions, and that the combination of these methods can substantially improve the sensitivity of the domain boundary prediction. This finding should enable the identification of novel structural domains, yielding new targets for large scale protein analyses

Visualization and Characterization of Cerebrospinal Fluid Motion Based on Magnetic Resonance Imaging

Purpose: To characterize cardiac- and respiratory-driven cerebrospinal fluid (CSF) motions in intracranial space noninvasively, four-dimensional velocity mapping (4D-VM), correlation mapping, and power and frequency mapping with cardiac-gated and/or asynchronous magnetic resonance (MR) phase contrast (PC) techniques were conducted

Evaluating the index of panoramic X-ray image quality using K-means clustering method

Background A panoramic X-ray image is generally considered optimal when the occlusal plane is slightly arched, presenting with a gentle curve. However, the ideal angle of the occlusal plane has not been determined. This study provides a simple evaluation index for panoramic X-ray image quality, built using various image and cluster analyzes, which can be used as a training tool for radiological technologists and as a reference for image quality improvement. Results A reference panoramic X-ray image was acquired using a phantom with the Frankfurt plane positioned horizontally, centered in the middle, and frontal plane centered on the canine teeth. Other images with positioning errors were acquired with anteroposterior shifts, vertical rotations of the Frankfurt plane, and horizontal left/right rotations. The reference and positioning-error images were evaluated with the cross-correlation coefficients for the occlusal plane profile, left/right angle difference, peak signal-to-noise ratio (PSNR), and deformation vector fields (DVF). The results of the image analyzes were scored for positioning-error images using K-means clustering analysis. Next, we analyzed the correlations between the total score, cross-correlation analysis of the occlusal plane curves, left/right angle difference, PSNR, and DVF. In the scoring, the positioning-error images with the highest quality were the ones with posterior shifts of 1 mm. In the analysis of the correlations between each pair of results, the strongest correlations (r = 0.7–0.9) were between all combinations of PSNR, DVF, and total score. Conclusions The scoring of positioning-error images using K-means clustering analysis is a valid evaluation indicator of correct patient positioning for technologists in training

Objective evaluation method using multiple image analyses for panoramic radiography improvement

Introduction: In the standardization of panoramic radiography quality, the education and training of beginners on panoramic radiographic imaging are important. We evaluated the relationship between positioning error factors and multiple image analysis results for reproducible panoramic radiography. Material and methods: Using a panoramic radiography system and a dental phantom, reference images were acquired on the Frankfurt plane along the horizontal direction, midsagittal plane along the left-right direction, and for the canine on the forward-backward plane. Images with positioning errors were acquired with 1-5 mm shifts along the forward-backward direction and 2-10 degrees rotations along the horizontal (chin tipped high/low) and vertical (left-right side tilt) directions on the Frankfurt plane. The cross-correlation coefficient and angle difference of the occlusion congruent plane profile between the reference and positioning error images, peak signal-to-noise ratio (PSNR), and deformation vector value by deformable image registration were compared and evaluated. Results: The cross-correlation coefficients of the occlusal plane profiles showed the greatest change in the chin tipped high images and became negatively correlated from 6 degrees image rotation (r = -0.29). The angle difference tended to shift substantially with increasing positioning error, with an angle difference of 8.9 degrees for the 10 degrees chin tipped low image. The PSNR was above 30 dB only for images with a 1-mm backward shift. The positioning error owing to the vertical rotation was the largest for the deformation vector value. Conclusions: Multiple image analyses allow to determine factors contributing to positioning errors in panoramic radiography and may enable error correction. This study based on phantom imaging can support the education of beginners regarding panoramic radiography

Convergence Stability of Depth-Depth-Matching-Based Steepest Descent Method in Simulated Liver Surgery

We recently established that our digital potential function was globally stable at the point where a virtual liver coincided with its real counterpart. In particular, because three rotational degrees of freedom are frequently used in a surgical operation on a real liver, stability of the potential function concerning three rotational degrees of freedom was carefully verified in the laboratory, using fluorescent lamps and sunlight. We achieved the same stability for several simulated liver operations using a 3D printed viscoelastic liver in a surgical operating room equipped with two light-emitting diode shadowless lamps. As a result, with increasing number of lamps, stability of our depth-depth matching in the steepest descendent algorithm improved because the lamps did not emit an infrared spectrum such as the one emitted by our depth camera. Furthermore, the slower the angular velocity in a surgical sequence, the more overall stability improved

Palladium-catalyzed regioselective and stereo-invertive ring-opening borylation of 2-arylaziridines with bis(pinacolato)diboron: Experimental and computational studies

A palladium catalyzed regioselective borylative ring opening reaction of 2-arylaziridines to give β-amino-β-arylethylborates was developed. The reaction reported herein represents the first example of ring-opening borylation of non-vinylic aziridines and direct borylative C(sp3)-N bond cleavage of neutral organic substrates. NMR studies and density functional theory (DFT) calculations suggested that the active intermediate for the reaction is a PdL2 complex [L = P(t-Bu)2Me]. The multi-component artificial force-induced reaction method (MC-AFIR) located the transition states for the regioselectivity-determining aziridine ring opening that proceeds in an SN2 fashion, and explained the selectivity of the reaction. The full catalytic cycle consists of a selectivity-determining aziridine ring opening (oxidative addition), a proton transfer, phosphine ligand dissociation from the catalyst, boron-boron bond cleavage, and reductive elimination. Water is important to the drive the transmetalation step. The calculated overall mechanism and selectivity are consistent with the experimental results

Local viscosity change in water near a solid-liquid interface and its extraction by means of molecular rotational diffusion : A molecular dynamics study

The relation between the rotational diffusion (RD) coefficient of water molecules and viscosity, that theoretically are inversely proportional to each other, was examined by using molecular dynamics simulations. In a homogeneous bulk liquid system, both the viscosity calculated from the virial theorem and the experimental one correlated well with the inverse of water RD coefficient at various temperatures. In a heterogeneous system of water between solid walls with different solid-liquid interaction strength, the viscosity distribution was similar to the distribution of the RD coefficient inverse multiplied by density, and this suggests the possibility of extracting nanometer-scale viscosity distribution by RD.Satoshi Nakaoka, Donatas Surblys, Yasutaka Yamaguchi, Koji Kuroda, Tadashi Nakajima, Hideo Fujimura, Local viscosity change in water near a solid–liquid interface and its extraction by means of molecular rotational diffusion – A molecular dynamics study, Chemical Physics Letters, Volume 591, 2014, Pages 306-311, https://doi.org/10.1016/j.cplett.2013.11.047