• Interdisciplinary Bio Central
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• v.3 no.4
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• pp.14.1-14.9
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• 2011

Protein homology detection is an important issue in comparative genomics. Because of the exponential growth of sequence databases, fast and efficient homology detection tools are urgently needed. Currently, for homology detection, sequence comparison methods using local alignment such as BLAST are generally used as they give a reasonable measure for sequence similarity. However, these methods have drawbacks in offering overall sequence similarity, especially in dealing with eukaryotic genomes that often contain many insertions and duplications on sequences. Also these methods do not provide the explicit models for speciation, thus it is difficult to interpret their similarity measure into homology detection. Here, we present a novel method based on Word Conservation Score (WCS) to address the current limitations of homology detection. Instead of counting each amino acid, we adopted the concept of 'Word' to compare sequences. WCS measures overall sequence similarity by comparing word contents, which is much faster than BLAST comparisons. Furthermore, evolutionary distance between homologous sequences could be measured by WCS. Therefore, we expect that sequence comparison with WCS is useful for the multiple-species-comparisons of large genomes. In the performance comparisons on protein structural classifications, our method showed a considerable improvement over BLAST. Our method found bigger micro-syntenic blocks which consist of orthologs with conserved gene order. By testing on various datasets, we showed that WCS gives faster and better overall similarity measure compared to BLAST.

• Journal of the Korean Geotechnical Society
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• v.18 no.5
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• pp.271-280
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• 2002

A probabilistic approach to identify the effects of uncertainties of soil strength parameters on searching a critical slip surface with the lowest reliability is introduced. In general construction field, it is impossible for the engineer to always gather a variety of statistical information of soil strength parameters for which lots of laboratory and in-situ soil testing are required and to use it with enough statistical knowledge. Thus, in order that the engineer may easily understand the probabilistic concept for the slope stability analysis, this study proposes a combined procedure to incorporate the engineering probabilistic tools into the existing deterministic slope stability analysis methods. Using UTEXAS 3, a slope stability analysis computer program developed by U.S. Army Corps of Engineers (U.S. COE), this study provides the results of this probabilistic slope stability analysis in terms of probability of failure or reliability index. This probabilistic method f3r slope stability analysis appears to yield more comprehensive results of slope reliability than does existing deterministic methods with safety factors alone.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.41 no.10
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• pp.997-1004
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• 2017

The life of elevator wire ropes is one of the most important characteristics of an elevator, which is closely related to the safety of users and its maintenance policy. It is not cost effective to measure the lifetime of elevator wire ropes during their use. In this study, the life estimation of elevator wire ropes (8x19W-IWRC) is considered using accelerated degradation test data. A bending fatigue tester is used to perform the accelerated degradation tests, incorporating the acceleration factor of tensile force. Assuming that the life of wire ropes is log-normally distributed, two life estimation methods are suggested and their results are compared. The first method estimates the life of wire ropes utilizing the accelerated life model with pseudo lives obtained from a linear regression model. The second method estimates the life using a logistic model based on failure probability.

• Proceedings of the Korea Water Resources Association Conference
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• 2015.05a
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• pp.244-244
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• 2015

Managed Aquifer Recharge (MAR) in the form of Aquifer Storage and Recovery (ASR) systems are being applied for numerous water augmentation projects both in developed and developing countries. Given the onset of Climate Change and its influence on weather patterns and land use, it has been acknowledged the utilization of this technology will be ever increasing. This technique like all others does have its drawbacks or disadvantages, whereby to overcome these drawbacks or disadvantages it is recommended that logical planning process be followed. In this study, we developed a decision framework known as "Decision framework for the planning, designing, construction/testing and implementation of subsurface water storage system" to further standardize the planning and design process of subsurface water storage system to increase the probability of having a successful ASR/ASTR project. The formulation of this framework was based on earlier frameworks, guidelines, published papers and technical reports which were compiled into a data collection database. The database of which consider both qualitative and quantitative aspect for example recharge objectives, site location, water chemistry of the native, source and recovered water, aquifer characteristics(hydraulic conductivity, transmissivity, porosity), injection/pumping rate, ecological constraints, societal restrictions, regulatory restrictions etc. The assimilation of these factors into a singular framework will benefit the broad spectrum of stakeholder as it maps the chronological order under which ASR project should be undertaken highlighting at each stage the feasibility of the project. The final stage of which should result in fully operational ASR system. The framework was applied to two case studies and through the application of a modified ASR site selection suitability index (Brown et al., 2005) a score was derived to identify the performance of each site. A high score of which meant a maximize chance of success given the reduce presence of project constraints.

• Coupled systems mechanics
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• v.4 no.4
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• pp.297-316
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• 2015

The use of fragility curves in the design of bridges is becoming common these days. In this study, experimental data have been used to develop fragility curves for the potential of girder unseating of a three-segment bridge and a bridge-abutment system including the influence of spatially varying ground motions, pounding, and abutment movement. The ground excitations were simulated based on the design spectra for different soil conditions. The Newmarket Viaduct replacement bridge in Auckland was used as the prototype bridge. These fragility curves were also applied to the 2010 Darfield and 2011 Christchurch earthquakes. The study showed that for bridges with similar characteristics as the chosen prototype and with similar fundamental frequencies, pounding could increase the probability of girder unseating by up to 35% and 30% based on the AASHTO and NZTA seating length requirements, respectively. The assumption of uniform ground excitations in many design practices, such as the NZTA requirements, could potentially be disastrous as girders might have a very good chance of unseating (as much as 53% higher chances when considering spatial variation of ground motions) even when they are designed not to. In the case of superstructures with dissimilar frequencies, the assumption of fixed abutments could significantly overestimate the girder unseating potential when pounding was ignored and underestimate the chances when pounding was considered. Bridges subjected to spatially varying ground excitations simulated based on the New Zealand design spectra for soft soil conditions with weak correlation shows the highest chances of girders falling off, of up to 65% greater than for shallow soil excitations.

• Journal of The Korean Astronomical Society
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• v.52 no.4
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• pp.133-144
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• 2019

We develop forecast models of daily probabilities of major flares (M- and X-class) based on empirical relationships between photospheric magnetic parameters and daily flaring rates from May 2010 to April 2018. In this study, we consider ten magnetic parameters characterizing size, distribution, and non-potentiality of vector magnetic fields from Solar Dynamics Observatory (SDO)/Helioseismic and Magnetic Imager (HMI) and Geostationary Operational Environmental Satellites (GOES) X-ray flare data. The magnetic parameters are classified into three types: the total unsigned parameters, the total signed parameters, and the mean parameters. We divide the data into two sets chronologically: 70% for training and 30% for testing. The empirical relationships between the parameters and flaring rates are used to predict flare occurrence probabilities for a given magnetic parameter value. Major results of this study are as follows. First, major flare occurrence rates are well correlated with ten parameters having correlation coefficients above 0.85. Second, logarithmic values of flaring rates are well approximated by linear equations. Third, using total unsigned and signed parameters achieved better performance for predicting flares than the mean parameters in terms of verification measures of probabilistic and converted binary forecasts. We conclude that the total quantity of non-potentiality of magnetic fields is crucial for flare forecasting among the magnetic parameters considered in this study. When this model is applied for operational use, it can be used using the data of 21:00 TAI with a slight underestimation of 2-6.3%.

• Journal of Pharmacopuncture
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• v.22 no.2
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• pp.83-89
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• 2019

Introduction: Oxidative stress (OS) during uncontrolled hyperglycemia has a pivotal role in pancreatic dysfunction. Our study aimed to demonstrate that crocin can potentiate anti-oxidant defense systems of pancreatic cells to improve oxidative stress. Methods: Male Wistar rats were divided randomly into four groups: a normal group, a normal-treated group, a diabetic group and a diabetic-treated group (n = 6 rats per group). Diabetes was induced by a single dose of streptozotocin (45 mg/kg/IV). The treated groups received crocin daily for 8 weeks (40 mg/kg/IP). At the end of the experiment, rats were sacrificed and pancreas tissue was obtained. Subsequently, the concentrations of malondialdehyde (MDA), nitrate and glutathione as well as the enzymatic activities of catalase and superoxide dismutase (SOD) were determined in all animals. Data were analyzed by two-way ANOVA with appropriate post hoc testing and a probability value of P < 0.05 was considered to represent a statistically significant difference in mean values. Results: Uncontrolled hyperglycemia weakened the anti-oxidant system by decreasing SOD and catalase enzyme activity in pancreatic tissues and induced OS by increasing the MDA content in diabetic non-treated animals. Crocin potentiated the anti-oxidant defense system by increasing the activity of both SOD and catalase, and improved OS by diminishing MDA production in pancreatic cells of rats contained in the diabetic-treated group. Conclusion: Based on our results, it is concluded that uncontrolled hyperglycemia can weaken the anti-oxidant defense system and cause the development of OS. Also, crocin can improve OS in pancreatic cells by potentiating the anti-oxidant defense system.

• Journal of Dental Anesthesia and Pain Medicine
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• v.21 no.2
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• pp.139-153
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• 2021

Background: In anesthetic techniques, touching bones can cause needle bending. Theoretically, a needle should support such deflection without fracturing. However, it is possible that a needle may fracture depending on the quality and type of needle used. This study evaluated the physical, chemical, and micromorphological characteristics of long and short dental anesthetic needles, as well as the mechanical properties of flexural load and bending resistance when needles are subjected to different bending angles. Methods: Long and short needles (30G, Jets, Misawa, Selekto, Terumo, Unoject and 27G, Dencojet, Injex, Jets, Misawa, Procare, Setoject XL, Terumo) were evaluated. Scanning electron microscopy was used to evaluate the needle bevels and energy-dispersive X-ray spectroscopy was used for the chemical analysis of needle compositions. Flexural loading and bending strength assessments were performed using a universal testing machine by bending the needles (n = 5) to angles of 30°, 60°, or 90°, or until fracture occurred. Results: The Injex 27G, Jets 27G, and Septoject XL 27G needles were all less than 30 mm in length. There were small percentage variations in the chemical compositions of the needles. Superior smoothness was observed for the Unoject 30G needle, which exhibited the highest fracture resistance at 60°. The Jets 30G needle exhibited greater resistance to fractures at 90°. The Procare 27G needle exhibited the highest load resistance to bending, followed by the Septoject XL 27G needle, and both needles were tied for the lowest fracture resistance. No needle fractured when bent to 30° or at less than three bends to 60° or 90°. Conclusions: Greater needle resistance to bending increases the probability of early fracturing. Thinner and shorter needles are more resistant than longer and thicker needles. Performing a single bend does not result in any significant risk of fracture or obliterate the lumen, allowing for the continued passage of anesthetic liquid.

• Journal of Astronomy and Space Sciences
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• v.39 no.2
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• pp.43-50
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• 2022

The unified scheme of Seyfert galaxies hypothesizes that the observed differences between the two categories of Seyfert galaxies, type 1 (Sy1) and type 2 (Sy2) are merely due to the difference in the orientation of the toroidal shape of the obscuring material in the active galactic nuclei. We used in this paper, a sample consisting of 120 Seyfert galaxies at 1.40 × 10⁹ Hz in radio, 2.52 × 10¹⁷ Hz in X-ray and 2.52 × 10²³ Hz in γ-ray luminosities observed by the Fermi Large Area Telescope (Fermi-LAT) in order to test the unified scheme of radio-quiet Seyfert galaxies. Our main results are as follows: (i) We found that the distributions of multiwave luminosities (L_radio, L_X-ray, and L_γ-ray) of Sy1 and Sy2 are completely overlapped with up to a factor of 4. The principal component analysis result reveals that Sy1 and Sy2 also occupy the same parameter spaces, which agrees with the notion that Sy1 and Sy2 are the same class objects. A Kolmogorov-Smirnov test performed on the sub-samples indicates that the null hypothesis (both are from the same population) cannot be rejected with chance probability p ~ 0 and separation distance K = 0.013. This result supports the fact that there is no statistical difference between the properties of Sy1 and Sy2 (ii) We found that the coefficient of the best-fit linear regression equation between the common properties of Sy1 and Sy2 is significant (r > 0.50) which plausibly implies that Sy1 and Sy2 are the same type of objects observed at different viewing angle.

• Animal Bioscience
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• v.34 no.9
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• pp.1460-1465
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• 2021

Objective: The study aimed to evaluate the diversity of donkey populations by comparing with the diversity of Thoroughbred and Jeju Halla horses; identified breeding backgrounds can contribute to management and conservation of donkeys in South Korea. Methods: A total of 100 horse (50 Thoroughbreds and 50 Jeju Halla horses) and 79 donkeys samples were genotyped with 15 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20), to identify genetic diversity and relationships among horses and donkeys. Results: The observed number of alleles per locus ranged from 1 (ASB17, HMS1) to 14 (AHT5), with a mean value of 4.87, 8.00, and 5.87 in Thoroughbreds, Jeju Halla horses, and donkeys, respectively. Of the 15 markers, AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, and LEX3 loci had relatively high polymorphism information content (PIC) values (PIC>0.5) in these three populations. Mean levels of genetic variation were H_E = 0.6721 and H_O = 0.6600 in Thoroughbreds, H_E = 0.7898 and H_O = 0.7100 in Jeju Halla horses, and H_E = 0.5635 and H_O = 0.4861 in donkeys. Of the 15 loci in donkeys, three loci had negative inbreeding coefficients (FIS), with a moderate mean FIS (0.138). The FIS estimate for the HTG4 marker was highest (0.531) and HMS6 marker was lowest (-0.001). The total probability of exclusion value of 15 microsatellite loci was 0.9996 in donkeys. Conclusion: Genetic cluster analysis showed that the genetic relationship among 79 donkeys was generally consistent with pedigree records. Among the three breeds, donkeys and Thoroughbred horses formed clearly different groups, but the group of Jeju Halla horses overlapped with that of Thoroughbred horses, suggesting that the loci would be suitable for donkey parentage testing. Therefore, the results of this study are a valid tool for genetic study and conservation of donkeys.