Identification of the antibacterial action mechanism of diterpenoids through transcriptome profiling

Effective antibacterial substances of Aralia continentalis have anti-biofilm and bactericidal activity to the oral pathogen Streptococcus mutans. In this study, three compounds extracted from A. continentalis were identified as acanthoic acid, continentalic acid, and kaurenoic acid by NMR and were further investigated how these diterpenoids affect the physiology of the S. mutans. When S. mutans was exposed to individual or mixed fraction of diterpenoids, severe growth defects and unique morphology were observed. The proportion of unsaturated fatty acids in the cell membrane was increased compared to that of saturated fatty acids in the presence of diterpenoids. Genome-wide gene expression profiles with RNA-seq were compared to reveal the mode of action of diterpenoids. Streptococcus mutans commonly enhanced the expression of 176 genes in the presence of the individual diterpenoids, whereas the expression of 232 genes was considerably reduced. The diterpenoid treatment modulated the expression of genes or operon(s) involved in cell membrane synthesis, cell division, and carbohydrate metabolism of S. mutans. Collectively, these findings provide novel insights into the antibacterial effect of diterpenoids to control S. mutans infection, which causes human dental caries

Three Factors to Improve Out-of-Distribution Detection

In the problem of out-of-distribution (OOD) detection, the usage of auxiliary data as outlier data for fine-tuning has demonstrated encouraging performance. However, previous methods have suffered from a trade-off between classification accuracy (ACC) and OOD detection performance (AUROC, FPR, AUPR). To improve this trade-off, we make three contributions: (i) Incorporating a self-knowledge distillation loss can enhance the accuracy of the network; (ii) Sampling semi-hard outlier data for training can improve OOD detection performance with minimal impact on accuracy; (iii) The introduction of our novel supervised contrastive learning can simultaneously improve OOD detection performance and the accuracy of the network. By incorporating all three factors, our approach enhances both accuracy and OOD detection performance by addressing the trade-off between classification and OOD detection. Our method achieves improvements over previous approaches in both performance metrics.Comment: Under revie

Sodium Biphenyl as Anolyte for Sodium-Seawater Batteries

Sodium-based battery systems have recently attracted increasing research interest due to the abundant resources employed. Among various material candidates for the negative electrode, sodium metal provides the highest capacity of theoretically 1165 mAh g(-1) and a very low redox potential of -2.71 versus the standard hydrogen electrode. However, the high reactivity of sodium metal toward the commonly used electrolytes results in severe side reactions, including the evolution of gaseous decomposition products, and, in addition, the risk of dendritic sodium growth, potentially causing a disastrous short circuit of the cell. Herein, the use of sodium biphenyl (Na-BP) as anolyte for the Na-seawater batteries (Na-SWB) is investigated. The catholyte for the open-structured positive electrode is natural seawater with sodium cations dissolved therein. Remarkably, the significant electronic and ionic conductivities of the Na-BP anolyte enable a low overpotential for the sodium deposition upon charge, allowing for high capacity and excellent capacity retention for 80 cycles in full Na-SWB. Additionally, the Na-BP anolyte suppresses gas evolution and dendrite growth by forming a homogeneous surface layer on the metallic negative electrode

Iterative Soft Decoding Algorithm for DNA Storage Using Quality Score and Redecoding

Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error correcting codes (ECCs). Previous works on recovering the data from the sequenced DNA pool with errors have utilized hard decoding algorithms based on a majority decision rule. To improve the correction capability of ECCs and robustness of the DNA storage system, we propose a new iterative soft decoding algorithm, where soft information is obtained from FASTQ files and channel statistics. In particular, we propose a new formula for log-likelihood ratio (LLR) calculation using quality scores (Q-scores) and a redecoding method which may be suitable for the error correction and detection in the DNA sequencing area. Based on the widely adopted encoding scheme of the fountain code structure proposed by Erlich et al., we use three different sets of sequenced data to show consistency for the performance evaluation. The proposed soft decoding algorithm gives 2.3% ~ 7.0% improvement of the reading number reduction compared to the state-of-the-art decoding method and it is shown that it can deal with erroneous sequenced oligo reads with insertion and deletion errors

Smart city services over a global interoperable Internet-of-Things system: the smart parking case

This paper presents the implementation of a global smart parking use case that employs data streams coming from two different cities: Santander, in Spain, and Busan, in South Korea. In addition to the geographical distance, what is more important is that the platforms used in each of the cities for exposing their data are different. Santander's data is available through FIWARE-based interfaces while Busan's exposes oneM2M endpoints. The underlying Wise-IoT system used for the field trial, which is briefly described in this paper, addresses the challenge of fragmentation within IoT ecosystems by developing a novel framework to achieve global interoperability and mobility of IoT applications and devices. In this sense, the proof-of-concept implementation presented in this paper serves as a validator of Global IoT Services, enabling transparent user, and applications, roaming between the two cities involved in the pilot.This work has been supported by the European Union's H2020 Programme for research, technological development and demonstration within the project "Worldwide Interoperability for Semantics IoT" under grant agreement No 723156 and by the Institute for Information & communications Technology Promotion (IITP) grant funded by the Korea government (MSIT) (No.2016-0-00067, Wise-IoT

Multiple Functions of Nm23-H1 Are Regulated by Oxido-Reduction System

Nucleoside diphosphate kinase (NDPK, Nm23), a housekeeping enzyme, is known to be a multifunctional protein, acting as a metastasis suppressor, transactivation activity on c-myc, and regulating endocytosis. The cellular mechanisms regulating Nm23 functions are poorly understood. In this study, we identified the modifications and interacting proteins of Nm23-H1 in response to oxidative stress. We found that Cys109 in Nm23-H1 is oxidized to various oxidation states including intra- and inter-disulfide crosslinks, glutathionylation, and sulfonic acid formation in response to H2O2 treatment both in vivo and in vitro. The cross-linking sites and modifications of oxidized Nm23-H1 were identified by peptide sequencing using UPLC-ESI-q-TOF tandem MS. Glutathionylation and oxidation of Cys109 inhibited the NDPK enzymatic activity of Nm23-H1. We also found that thioredoxin reductase 1 (TrxR1) is an interacting protein of Nm23-H1, and it binds specifically to oxidized Nm23-H1. Oxidized Nm23 is a substrate of NADPH-TrxR1-thioredoxin shuttle system, and the disulfide crosslinking is reversibly reduced and the enzymatic activity is recovered by this system. Oxidation of Cys109 in Nm23-H1 inhibited its metastatic suppressor activity as well as the enzymatic activities. The mutant, Nm23-H1 C109A, retained both the enzymatic and metastasis suppressor activities under oxidative stress. This suggests that key enzymatic and metastasis suppressor functions of Nm23-H1 are regulated by oxido-reduction of its Cys109

Localized Laser-Based Photohydrothermal Synthesis of Functionalized Metal-Oxides

We discuss the rapid in situ hydrothermal synthesis of metal oxide materials based on the photothermal superheating of light-absorbing metal layers for simple and facile on-demand placement of semiconductor materials with micrometer-scale lateral resolution. Localized heating from pulsed and focused laser illumination enables ultrafast growth of metal oxide materials with high spatiotemporal precision in aqueous precursor solution. Among many possible electronic and optoelectronic applications, the proposed method can be used for laser-based in situ real-time soldering of separated metal structures and electrodes with functionalized semiconductor materials. Resistive electrical interconnections of metal strip lines as well as sensitive UV detection using photohydrothermally grown metal oxide bumps are experimentally demonstrated

MOD(i) : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra

MOD(i) () is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in a peptide. It is powerful in that it can interpret a tandem mass spectrum even when hundreds of modification types are considered and the number of potential PTMs in a peptide is large, in contrast to most of the methods currently available for spectra interpretation that limit the number of PTM sites and types being used for PTM analysis. For example, using MOD(i), one can consider for analysis both the entire PTM list published on the unimod webpage () and user-defined PTMs simultaneously, and one can also identify multiple PTM sites in a spectrum. MOD(i) is convenient in that it can take various input file formats such as .mzXML, .dta, .pkl and .mgf files, and it is equipped with a graphical tool called MassPective developed to display MOD(i)'s output in a user-friendly manner and helps users understand MOD(i)'s output quickly. In addition, one can perform manual de novo sequencing using MassPective

Efficient Perovskite Light-Emitting Diodes Using Polycrystalline Core-Shell-Mimicked Nanograins

Making small nanograins in polycrystalline organic-inorganic halide perovskite (OIHP) films is critical to improving the luminescent efficiency in perovskite light-emitting diodes (PeLEDs). 3D polycrystalline OIHPs have fundamental limitations related to exciton binding energy and exciton diffusion length. At the same time, passivating the defects at the grain boundaries is also critical when the grain size becomes smaller. Molecular additives can be incorporated to shield the nanograins to suppress defects at grain boundaries; however, unevenly distributed molecular additives can cause imbalanced charge distribution and inefficient local defect passivation in polycrystalline OIHP films. Here, a kinetically controlled polycrystalline organic-shielded nanograin (OSN) film with a uniformly distributed organic semiconducting additive (2,2 ',2 ''-(1,3,5-benzinetriyl)-tris(1-phenyl-1-H-benzimidazole), TPBI) is developed mimicking core-shell nanoparticles. The OSN film causes improved photophysical and electroluminescent properties with improved light out-coupling by possessing a low refractive index. Finally, highly improved electroluminescent efficiencies of 21.81% ph el(-1) and 87.35 cd A(-1) are achieved with a half-sphere lens and four-time increased half-lifetime in polycrystalline PeLEDs. This strategy to make homogeneous, defect-healed polycrystalline core-shell-mimicked nanograin film with better optical out-coupling will provide a simple and efficient way to make highly efficient perovskite polycrystal films and their optoelectronics devices.