Predicting and improving the protein sequence alignment quality by support vector regression

Abstract Background For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significantly depending on our choice of various alignment parameters such as gap opening penalty and gap extension penalty. Because the accuracy of sequence alignment is typically measured by comparing it with its corresponding structure alignment, there is no good way of evaluating alignment accuracy without knowing the structure of a query protein, which is obviously not available at the time of structure prediction. Moreover, there is no universal alignment parameter option that would always yield the optimal alignment. Results In this work, we develop a method to predict the quality of the alignment between a query and a template. We train the support vector regression (SVR) models to predict the MaxSub scores as a measure of alignment quality. The alignment between a query protein and a template of length n is transformed into a (n + 1)-dimensional feature vector, then it is used as an input to predict the alignment quality by the trained SVR model. Performance of our work is evaluated by various measures including Pearson correlation coefficient between the observed and predicted MaxSub scores. Result shows high correlation coefficient of 0.945. For a pair of query and template, 48 alignments are generated by changing alignment options. Trained SVR models are then applied to predict the MaxSub scores of those and to select the best alignment option which is chosen specifically to the query-template pair. This adaptive selection procedure results in 7.4% improvement of MaxSub scores, compared to those when the single best parameter option is used for all query-template pairs. Conclusion The present work demonstrates that the alignment quality can be predicted with reasonable accuracy. Our method is useful not only for selecting the optimal alignment parameters for a chosen template based on predicted alignment quality, but also for filtering out problematic templates that are not suitable for structure prediction due to poor alignment accuracy. This is implemented as a part in FORECAST, the server for fold-recognition and is freely available on the web at http://pbil.kaist.ac.kr/forecast</p

Patient Perception of Natural Orifice Transluminal Endoscopic Surgery in an Endoscopy Screening Program in Korea

Purpose Natural orifice transluminal endoscopic surgery (NOTES) is a new method of accessing intracavitary organs in order to minimize pain by avoiding incisions in the body wall. The aim of this study is to determine patients' acceptance of NOTES in Korea and to compare their views about laparoscopic surgery and NOTES for benign and malignant diseases. Materials and Methods The target number of total subjects was calculated to be 540. The subjects were classified into 18 sub-groups based on age groups, gender, and history of prior surgery. The questionnaire elicited information about demographic characteristics, medical check-ups, diseases, endoscopic and surgical histories, marital status and childbirth, the acceptance of NOTES, and the preferred routes for NOTES. In addition, the subjects chose laparoscopic surgery or NOTES for a hypothetical cholecystectomy and rectal cancer surgery, and responded to questions regarding the acceptable complication rate of NOTES, the appropriate cost of NOTES, and the reason(s) why they did not select NOTES. Results: 486 of 540 patients (90.0%) who agreed to participate in this study completed the questionnaire. NOTES was preferred by the following patients: elderly; a history of treatment due to a disease; having regular check-ups; and a history of an endoscopic procedure (p<0.05). The most preferred route for NOTES was the stomach (67.1%). Eighty-four percent of the patients choosing NOTES responded that the complication rate of the new surgical method should be the same or lower than laparoscopic surgery. Vague anxiety over a new surgical method was the most common reason why NOTES was not selected in benign and malignant diseases (64% and 73%), respectively. Conclusion: Patients appear to be interested in the potential benefits of NOTES and would embrace it if their concerns about safety are met. We believe that qualified surgical endoscopists can meet these safety concerns, and that NOTES development has the potential to flourish

Accelerating universe in two-dimensional noncommutative dilaton cosmology

We show that the phase transition from the decelerating universe to the accelerating universe, which is of relevance to the cosmological coincidence problem, is possible in the semiclassically quantized two-dimensional dilaton gravity by taking into account the noncommutative field variables during the finite time. Initially, the quantum-mechanically induced energy from the noncommutativity among the fields makes the early universe decelerate and subsequently the universe is accelerating because the dilaton driven cosmology becomes dominant later.Comment: 14 pages, 2 figures; to appear in Phys. Lett.

Shear-solvo defect annihilation of diblock copolymer thin films over a large area

Achieving defect-free block copolymer (BCP) nanopatterns with a long-ranged orientation over a large area remains a persistent challenge, impeding the successful and widespread application of BCP self-assembly. Here, we demonstrate a new experimental strategy for defect annihilation while conserving structural order and enhancing uniformity of nanopatterns. Sequential shear alignment and solvent vapor annealing generate perfectly aligned nanopatterns with a low defect density over centimeter-scale areas, outperforming previous single or sequential combinations of annealing. The enhanced order quality and pattern uniformity were characterized in unprecedented detail via scattering analysis and incorporating new mathematical indices using elaborate image processing algorithms. In addition, using an advanced sampling method combined with a coarse-grained molecular simulation, we found that domain swelling is the driving force for enhanced defect annihilation. The superior quality of large-scale nanopatterns was further confirmed with diffraction and optical properties after metallized patterns, suggesting strong potential for application in optoelectrical devices

FEASIBILITY STUDY ON EFFECT OF STRUCTURAL FLEXIBILITY OF ASYMMETRIC PRE-SWIRL STATOR ON PROPULSION PERFORMANCE FOR KRISO CONTAINER SHIP (KCS)

The use of energy-saving devices is the most effective method for decreasing CO2 emissions, which is an increasingly concerning environmental issue. The asymmetric pre-swirl stator has been developed as an energy-saving device and has been successfully applied to various types of vessels. In the present study, a flexible material was applied to an asymmetric pre-swirl stator to determine the variation in the flow around stator and its efficiency. A fluid–structure interaction (FSI) analysis system was developed using the Star-CCM+ (fluid) and the Abaqus (structure). The proposed analysis system was validated by comparing the experimental results using a flexible plate in a flowing fluid. The flexible stator was applied to a 3,600 TEU KRISO Container Ship to determine the improvement in its performance compared to the previous optimum value achieved with a rigid stator. Although this application was conducted on a model scale and the deformation was small, the results of the flexible stator indicated the possibility of not only increasing the efficiency but also decreasing the vortex risk around stator blade

Geomagnetic field influences probabilistic abstract decision-making in humans

To resolve disputes or determine the order of things, people commonly use binary choices such as tossing a coin, even though it is obscure whether the empirical probability equals to the theoretical probability. The geomagnetic field (GMF) is broadly applied as a sensory cue for various movements in many organisms including humans, although our understanding is limited. Here we reveal a GMF-modulated probabilistic abstract decision-making in humans and the underlying mechanism, exploiting the zero-sum binary stone choice of Go game as a proof-of-principle. The large-scale data analyses of professional Go matches and in situ stone choice games showed that the empirical probabilities of the stone selections were remarkably different from the theoretical probability. In laboratory experiments, experimental probability in the decision-making was significantly influenced by GMF conditions and specific magnetic resonance frequency. Time series and stepwise systematic analyses pinpointed the intentionally uncontrollable decision-making as a primary modulating target. Notably, the continuum of GMF lines and anisotropic magnetic interplay between players were crucial to influence the magnetic field resonance-mediated abstract decision-making. Our findings provide unique insights into the impact of sensing GMF in decision-makings at tipping points and the quantum mechanical mechanism for manifesting the gap between theoretical and empirical probability in 3-dimensional living space.Comment: 32 pages, 5 figures, 4 supplementary figures, 2 supplementary tables, and separate 15 ancillary file

Reliability Verification of the Performance Evaluation of Multiphase Pump

The crude oil in an oil well exists in various phases such as gas, seawater, and sand, as well as oil. Therefore, a phase separator is needed at the front of a single-phase pump for pressurization and transfer. On the other hand, the application of a multiphase pump can provide such advantages as simplification of the equipment structure and cost savings, because there is no need for a phase separation process. Therefore, the crude oil transfer method using a multiphase pump is being applied to recently developed oil wells. Due to this increase in demand, technical demands for the development of multiphase pumps are sharply increasing, but the progress of research into related technologies is insufficient, due to the nature of multiphase pumps that require high levels of skills. This study was conducted to verify the reliability of pump performance evaluation using numerical analysis, which is the basis of the development of a multiphase pump. For this study, a model was designed by selecting the specifications of the pump under study. The performance of the designed model was evaluated through numerical analysis and experiment, and the results of the performance evaluation were compared to verify the reliability of the result using numerical analysis

Enhanced magnetic and thermoelectric properties in epitaxial polycrystalline SrRuO3 thin film

Transition metal oxide thin films show versatile electrical, magnetic, and thermal properties which can be tailored by deliberately introducing macroscopic grain boundaries via polycrystalline solids. In this study, we focus on the modification of the magnetic and thermal transport properties by fabricating single- and polycrystalline epitaxial SrRuO3 thin films using pulsed laser epitaxy. Using epitaxial stabilization technique with atomically flat polycrystalline SrTiO3 substrate, epitaxial polycrystalline SrRuO3 thin film with crystalline quality of each grain comparable to that of single-crystalline counterpart is realized. In particular, alleviated compressive strain near the grain boundaries due to coalescence is evidenced structurally, which induced enhancement of ferromagnetic ordering of the polycrystalline epitaxial thin film. The structural variations associated with the grain boundaries further reduce the thermal conductivity without deteriorating the electronic transport, and lead to enhanced thermoelectric efficiency in the epitaxial polycrystalline thin films, compared with their single-crystalline counterpart.Comment: 24 pages, 5 figure

Fabrication of Complex 3D Micro-Scale Scaffolds and Drug Delivery Devices using Dynamic Mask Projection Microstereolithography

Microstereolithography (μSL) technology can fabricate three-dimensional (3D) tissue engineered scaffolds with controlled biochemical and mechanical micro-architectures. A μSL system for tissue engineering was developed using a Digital Micromirror Device (DMDTM) for dynamic pattern generation and an ultraviolet (UV) lamp filtered at 365 nm for crosslinking the photoreactive polymer solution. The μSL system was designed with x-y resolution of ~2 μm and a vertical (z) resolution of ~1 μm. To demonstrate the use of μSL in tissue engineering, poly(propylene fumarate) (PPF) was synthesized with a molecular weight of ~1200 Da. The viscosity of the PPF was reduced to ~150 cP (at 50 o C) by mixing with diethyl fumarate (DEF) in the ratio of 7:3 (w/w). Finally, ~2 % (w/w) of (bis(2,4,6- trimethylbenzoyl) phenylphosphine oxide (BAPO) was added to the solution to serve as a photoinitiator. Cure depth experiments were performed to determine the curing characteristics of the synthesized PPF, and the resulting system and photopolymer were used to construct a variety of 3D porous scaffolds with interconnected pores between 100 and 150 μm and a micro-needle array with height of ~800 μm and individual tip diameters of ~20 μm. SEM and microscope images of the micro-architectures illustrate that the developed μSL system is a promising technology for producing biodegradable and biocompatible microstructures.Mechanical Engineerin