Showing papers by "Dong-Wook Kim published in 2021"

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity.

Abstract: The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and multiple studies have proposed its application in prokaryotic taxonomy and related disciplines. AAI demonstrates better resolution in elucidating taxonomic structure beyond the species rank when compared with average nucleotide identity (ANI), which is a standard criterion in species delineation. However, an efficient and easy-to-use computational tool for AAI calculation in large-scale taxonomic studies is not yet available. Here, we introduce a bioinformatic pipeline, named EzAAI, which allows for rapid and accurate AAI calculation in prokaryote sequences. The EzAAI tool is based on the MMSeqs2 program and computes AAI values almost identical to those generated by the standard BLAST algorithm with significant improvements in the speed of these evaluations. Our pipeline also provides a function for hierarchical clustering to create dendrograms, which is an essential part of any taxonomic study. EzAAI is available for download as a standalone JAVA program at http://leb.snu.ac.kr/ezaai .

Review of machine learning methods in soft robotics

Abstract: Soft robots have been extensively researched due to their flexible, deformable, and adaptive characteristics. However, compared to rigid robots, soft robots have issues in modeling, calibration, and control in that the innate characteristics of the soft materials can cause complex behaviors due to non-linearity and hysteresis. To overcome these limitations, recent studies have applied various approaches based on machine learning. This paper presents existing machine learning techniques in the soft robotic fields and categorizes the implementation of machine learning approaches in different soft robotic applications, which include soft sensors, soft actuators, and applications such as soft wearable robots. An analysis of the trends of different machine learning approaches with respect to different types of soft robot applications is presented; in addition to the current limitations in the research field, followed by a summary of the existing machine learning methods for soft robots.

UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis.

Abstract: Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2 .

Drastic change of magnetic anisotropy in Fe3GeTe2 and Fe4GeTe2 monolayers under electric field studied by density functional theory.

Abstract: Magnetic anisotropy energy (MAE) is one of the most important properties in two-dimensional magnetism since the magnetization in two dimension is vulnerable to the spin rotational fluctuations. Using density functional theory calculation, we show that perpendicular electric field dramatically enhances the in-plane and out-of-plane magnetic anisotropies in Fe3GeTe2 and Fe4GeTe2 monolayers, respectively, allowing the change of easy axis in both systems. The changes of the MAE under the electric field are understood as the result of charge redistribution inside the layer, which is available due to the three-dimensional (3D) network of Fe atoms in the monolayers. As a result, we suggest that due to the unique structure of FenGeTe2 compounds composed by peculiar 3D networks of metal atoms, the MAE can be dramatically changed by the external perpendicular electric field.

VicPred: A Vibrio cholerae Genotype Prediction Tool.

Abstract: Genomic information can be used to predict major pathogenic traits of pathogens without the need for laboratory experimentation. However, no Vibrio cholerae genome-based trait identification tools currently exist. The aim of this study was to develop a web-based prediction tool to identify Vibrio pathogenic traits using publicly available 796 whole-genome sequences of V. cholerae. Using this application, 68 structural O-antigen gene clusters belonging to 49 serogroups of V. cholerae were classified, and the composition of the genes within the O-antigen cluster of each serogroup was identified. The arrangement and location of the CTX prophage, and related elements of the seventh cholera pandemic strains were also revealed. With the versatile tool, named VicPred, we analyzed the assemblage of various SXTs (sulfamethoxazole/trimethoprim resistance element) and major genomic islands (GIs) of V. cholerae, and the increasing trend in drug-resistance revealing high resistance of the V. cholerae strains to certain antibiotics. The pathogenic traits of newly sequenced V. cholerae strains could be analyzed based on these characteristics. The accumulation of further genome data will expedite the establishment of a more precise genome-based pathogenic traits analysis tool.

Printed Stretchable Single-Nanofiber Interconnections for Individually-Addressable Highly-Integrated Transparent Stretchable Field Effect Transistor Array.

Abstract: Stretchable electronics have been spotlighted as promising next-generation electronics. In order to drive a specific unit device in an integrated stretchable device, the interconnection of the device should be placed in a desired position and addressed individually. In addition, practical stretchable interconnection requires reliable stretchability, high conductivity, optical transparency, high resolution, and fast and large-scale production. This study proposes an approach to meet these requirements. We print the single wavy polymer nanofibers (NFs) in a desired position and convert them into metal NF interconnections. The nanoscale diameter and the wavy cylindrical shape of the metal NFs are the main reasons for the reliable stretchability and the excellent transparency. Using the stretchable metal NFs and the stretchable organic semiconductor NFs, an array of all-stretchable transparent NF-field effect transistors (NF-FETs) is demonstrated. The highly integrated NF-FET array (10 FETs/mm2) shows uniform performance and good stability under repeated severe mechanical deformations.

Pairing Forces Govern Population of Doubly Magic ^{54}Ca from Direct Reactions.

Abstract: Direct proton-knockout reactions of ^{55}Sc at ∼220 MeV/nucleon were studied at the RIKEN Radioactive Isotope Beam Factory. Populated states of ^{54}Ca were investigated through γ-ray and invariant-mass spectroscopy. Level energies were calculated from the nuclear shell model employing a phenomenological internucleon interaction. Theoretical cross sections to states were calculated from distorted-wave impulse approximation estimates multiplied by the shell model spectroscopic factors, which describe the wave function overlap of the ^{55}Sc ground state with states in ^{54}Ca. Despite the calculations showing a significant amplitude of excited neutron configurations in the ground-state of ^{55}Sc, valence proton removals populated predominantly the ground state of ^{54}Ca. This counterintuitive result is attributed to pairing effects leading to a dominance of the ground-state spectroscopic factor. Owing to the ubiquity of the pairing interaction, this argument should be generally applicable to direct knockout reactions from odd-even to even-even nuclei.

Direct observation of kink evolution due to Hund’s coupling on approach to metal-insulator transition in NiS2−xSex

Abstract: Understanding characteristic energy scales is a fundamentally important issue in the study of strongly correlated systems. In multiband systems, an energy scale is affected not only by the effective Coulomb interaction but also by the Hund's coupling. Direct observation of such energy scale has been elusive so far in spite of extensive studies. Here, we report the observation of a kink structure in the low energy dispersion of NiS2-xSex and its characteristic evolution with x, by using angle resolved photoemission spectroscopy. Dynamical mean field theory calculation combined with density functional theory confirms that this kink originates from Hund's coupling. We find that the abrupt deviation from the Fermi liquid behavior in the electron self-energy results in the kink feature at low energy scale and that the kink is directly related to the coherence-incoherence crossover temperature scale. Our results mark the direct observation of the evolution of the characteristic temperature scale via kink features in the spectral function, which is the hallmark of Hund's physics in the multiorbital system.

A Multi-Server Authentication Protocol Achieving Privacy Protection and Traceability for 5G Mobile Edge Computing

Abstract: Mobile Edge Computing (MEC) is placed near mobile devices in the form of edge servers to meet the requirements of time-sensitive applications, providing low-latency computing and data storage. As user privacy issues are considered one of the biggest issues in the MEC environment, there are various approaches for anonymous authentication. However, these are not ready for commercial applications due to a lack of user traceability for rewards, service fees, penalties, and so on. This paper proposes a user authentication protocol in the MEC environment that satisfied the two conflicting security requirements of user anonymity and traceability. The proposed protocol provides anonymous mutual authentication between mobile devices and application servers operating on MEC platform, while ensures that the trusted MEC server can securely track users on behalf of service providers.

Modeling and Mapping of Combined Noise Annoyance for Aircraft and Road Traffic Based on a Partial Loudness Model.

Abstract: Complex transportation systems often produce combined exposure to aircraft and road noise. Depending on the noise source, the annoyance response is different, and a masking effect occurs between the noise sources within the combined noise. Considering these characteristics, partial loudness was adopted to evaluate noise annoyance. First, a partial loudness model incorporating binaural inhibition was proposed and validated. Second, short- and long-term annoyance models were developed using partial loudness. Finally, the annoyance of combined noise was visualized as a map. These models can evaluate the annoyance by considering both the intensity and frequency characteristics of the noise. In addition, it is possible to quantify the masking effect that occurs between noise sources. Combined noise annoyance maps depict the degree of annoyance of residents and show the background noise effect, which is not seen on general noise maps.

Framework for Smart City Model Composition: Choice of Component Design Models and Risks

Abstract: This paper is a reflective overview of the knowledge on online conversion of services in the perspective of urban planning. It points that traditional planning aimed at building optimal spatial relationships between particular functions in urban environment. Appropriate decision-making rules had been introduced, contributing to a hierarchical land-use structure. This conventional approach has been recently challenged by the rapid ICT development which added a lively, virtual, non-spatial dimension of urban economy. The well-established foundations of urban planning started to shake, calling for a new paradigm. This paper looks for an alternative to traditional planning which would be able to develop policies for omnichannel services (i.e., enterprises that use both online and offline channels for communicating and distributing their products). The advantages of ‘e-planning' in managing omnichannel services are outlined and a conclusion is drawn that only a multi-channel approach can bring appropriate answers to contemporary developments in services sector.

Electronic structures and optical characteristics of fluorescent pyrazinoquinoxaline assemblies and Au interfaces.

Abstract: Understanding the excitonic processes at the interfaces of fluorescent π-conjugated molecules and metal electrodes is important for both fundamental studies and emerging applications. Adsorption configurations of molecules on metal surfaces significantly affect the physical characteristics of junctions as well as molecules. Here, the electronic structures and optical properties of molecular assemblies/Au interfaces were investigated using scanning probe and photoluminescence microscopy techniques. Scanning tunneling microscopy images and tunneling conductance spectra suggested that the self-assembled molecules were physisorbed on the Au surface. Visible-range photoluminescence studies showed that Au thin films modified the emission spectra and reduced the lifetime of excitons. Surface potential maps, obtained by Kelvin probe force microscopy, could visualize electron transfer from the molecules to Au under illumination, which could explain the decreased lifetime of excitons at the molecule/Au interface.

Rotator cuff retear after repair surgery: comparison between experienced and inexperienced surgeons.

Abstract: BACKGROUND We hypothesized in this study that the characteristics of retear cases vary according to surgeon volume and that surgical outcomes differ between primary and revision arthroscopic rotator cuff repair (revisional ARCR). METHODS Surgeons performing more than 12 rotator cuff repairs (RCRs) per year were defined as high-volume surgeons, and those performing fewer than 12 RCRs were considered low-volume surgeons. Of the 47 patients who underwent revisional ARCR at our clinic enrolled in this study, 21 cases were treated by high-volume surgeons and 26 cases by low-volume surgeons. In all cases, the interval between primary surgery and revisional ARCR, degree of "acromial scuffing," number of anchors, RCR technique, retear pattern, fatty infiltration, retear size, operating time, and clinical outcome were recorded. RESULTS During primary surgery, significantly more lateral anchors (p=0.004) were used, and the rate of use of the double-row repair technique was significantly higher (p<0.001) in the high- versus low-volume surgeon group. Moreover, the "cut-through pattern" was observed significantly more frequently among the cases treated by high- versus low-volume surgeons (p=0.008). The clinical outcomes after revisional ARCR were not different between the two groups. CONCLUSIONS Double-row repair during primary surgery and the cut-through pattern during revisional ARCR were more frequent in the high- versus low-volume surgeon groups. However, no differences in retear site or size, fatty infiltration grade, or outcomes were observed between the groups.

RGB images-based vegetative index for phenotyping kenaf (Hibiscus cannabinus L.).

Abstract: Kenaf (Hibiscus cannabinus L.) is an industrial crop used as a raw material in various fields and is cultivated worldwide. Compared to high potential for its utilization, breeding sector is not vigorous partially due to laborous breeding procedure. Thus, efficient breeding methods are required for varieties that can adapt to various environments and obtain optimal production. For that, identifying kenaf’s characteristics is very important during the breeding process. Here, we investigated if RGB based vegetative index (VI) could be associated with traits for biomass. We used 20 varieties and germplasm of kenaf and RGB images taken with unmanned aerial vehicles (UAVs) for field selection in early and late growth stage. In addition, measuring the stem diameter and the number of nodes confirmed whether the vegetative index value obtained from the RGB image could infer the actual plant biomass. Based on the results, it was confirmed that the individual surface area and estimated plant height, which were identified from the RGB image, had positive correlations with the stem diameter and node number, which are actual growth indicators of the rate of growth further, biomass could also be estimated based on this. Moreover, it is suggested that VIs have a high correlation with actual growth indicators; thus, the biomass of kenaf could be predicted. Interstingly, those traits showing high correlation in the late stage had very low correlations in the early stage. To sum up, the results in the current study suggest a more efficient breeding method by reducing labor and resources required for breeding selection by the use of RGB image analysis obtained by UAV. This means that considerable high-quality research could be performed even with a tight budget. Furthermore, this method could be applied to crop management, which is done with other vegetative indices using a multispectral camera.

Enhanced optical absorption in conformally grown MoS2 layers on SiO2/Si substrates with SiO2 nanopillars with a height of 50 nm

Abstract: The integration of transition metal dichalcogenide (TMDC) layers on nanostructures has attracted growing attention as a means to improve the physical properties of the ultrathin TMDC materials. In this work, the influence of SiO2 nanopillars (NPs) with a height of 50 nm on the optical characteristics of MoS2 layers is investigated. Using a metal organic chemical vapor deposition technique, a few layers of MoS2 were conformally grown on the NP-patterned SiO2/Si substrates without notable strain. The photoluminescence and Raman intensities of the MoS2 layers on the SiO2 NPs were larger than those observed from a flat SiO2 surface. For 100 nm-SiO2/Si wafers, the 50 nm-NP patterning enabled improved absorption in the MoS2 layers over the whole visible wavelength range. Optical simulations showed that a strong electric-field could be formed at the NP surface, which led to the enhanced absorption in the MoS2 layers. These results suggest a versatile strategy to realize high-efficiency TMDC-based optoelectronic devices.

Evaluation of Efficacy about Disinfectants in Biological Containment Facilities

Abstract: Department of Microbiology, Konkuk University College of Medicine, Seoul 05029, Republic of Korea Research Institute of Medical Science, Konkuk University College of Medicine, Seoul 05029, Republic of Korea Institute of Environmental Protection and Safety, Seoul National University, Seoul 08826, Republic of Korea International Vaccine Institute, Seoul 08826, Republic of Korea Woojungbio Company, Gyeonggi Province 16229, Republic of Korea

Pseudoequilibrium between Etching and Selective Grain Growth: Chemical Conversion of a Randomly Oriented Au Film into a (111)-Oriented Ultrathin Au Film.

Abstract: Metal thin films with a specific orientation play vital roles in electronics, catalysts, and epitaxial templates. Although oriented metal films have been produced in the recent years, ultrathin oriented metal films (<10 nm) have not been achieved owing to the interfacial instability of the ultrathin films during the thermal annealing process. This study investigates chemical conversion of randomly oriented multigrain Au ultrathin films into (111)-oriented Au ultrathin films. A novel chemical process, termed pseudoequilibrium of etching and selective grain growth, is presented for the chemical conversion by using a quaternary ammonium halide. The reaction variables (reaction time, reaction temperature, species of halide ions) for the chemical conversion process are systematically investigated. This study reveals the in-plane rotational degeneracy in the Au(111) thin film epitaxially grown on a Si(111) substrate. The chemical process can be applied to a broad range of thicknesses from 9 to 100 nm.

dg.o 2022: Opportunities and Risks in Intelligent Governance and Smart City

Abstract: With the advent of intelligent technologies such as AI-driven automations and IoT-based omni-sense intelligent society, it is imminent to identify the potentials and risks through research, development, and practices. The Center of Intelligent Society and Policy (CISP) at Seoul National University is a leading research center for studying the government's role and innovating policies for intelligent society and smart cities. In this workshop, we discuss the extensive research and development efforts in CISP and invite diverse background researchers to discuss and critically evaluate the potentials and the possible and unforeseen risks of the intelligent society. This workshop aims to identify the potential subtopic areas and sustainable factors for the next generation intelligent society as focal themes of dg.o 2022. We will briefly introduce the CISP, current research projects, and dg.o 2022 conference. We invite all interested scholars and practitioners and look forward to exchange ideas and take suggestions for collaboration and cooperation.

Modern pollen–climate relationships and their application for pollen-based quantitative climate reconstruction of the mid-Holocene on the southern Korean Peninsula

Abstract: A modern pollen dataset is a prerequisite for reconstructing quantitative paleoclimate and paleovegetation cover using fossil pollen records. Although multiple modern pollen–climate datasets have b...

Investigation of the ground-state spin inversion in the neutron-rich 47,49Cl isotopes

Abstract: A first gamma-ray study of 47,49Cl spectroscopy was performed at the Radioactive Isotope Beam Factory with 50Ar projectiles at 217 MeV/nucleon, impinging on the liquid hydrogen target of the MINOS device. Prompt de-excitation gamma-rays were measured with the NaI(Tl) array DALI2+. Through the one-proton knockout reaction 50Ar(p,2p), a spin assignment could be determined for the low-lying states of 49Cl from the momentum distribution obtained with the SAMURAI spectrometer. A spin-parity J = 3/2+ is deduced for the ground state of 49Cl, similar to the recently studied N = 32 isotope 51K.

23-valent polysaccharide vaccine (PPSV23)-targeted serotype-specific identification of Streptococcus pneumoniae using the loop-mediated isothermal amplification (LAMP) method.

Abstract: Reports of invasive disease due to Streptococcus pneumoniae have declined since the introduction of pneumococcal conjugate vaccines (PCV7 and PCV13). The incidence of invasive diseases due to S. pneumoniae that are not addressed by the vaccines, however, has increased in children and adults, creating a global public health problem. Previously, we established the loop-mediated isothermal amplification (LAMP) method for a PCV13 serotype-specific assay. In the current study, we developed a rapid, simple, and cost-effective assay to detect serotypes in the 23-valent pneumococcal polysaccharide vaccine (PPSV23) using the LAMP method. In this study, LAMP primer sets for serotypes 2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20, 22F, and 33F of S. pneumoniae were developed. The reactivity, specificity, and sensitivity of LAMP assays were determined and compared to those of conventional PCR. The feasibility of LAMP assays in clinical application in patients with invasive pneumococcal diseases was validated by defining the detection limit of the LAMP assay with bacterial genomic DNA-spiked blood specimens. The specificity of each LAMP assay was determined using 44 serotypes of pneumococcal strains. Their sensitivity was 100 copies per reaction versus 103 to 106 copies per reaction for PCR assays. Using DNA-spiked blood specimens, excluding the LAMP assay that targeted serotype 22F (103 copies per reaction), the limit of detection of the LAMP assay was similar to that with purified DNA as the template (102 copies per reaction), compared with 103 to >106 copies per reaction for PCR assays. In conclusion, a rapid and simple LAMP-based PPSV23-targeted serotype detection assay was developed for use in many countries. This study is the first report of a LAMP-based assay for identification of PPSV23 serotypes. Further evaluation of this assay is needed through surveillance and vaccine efficacy studies.