Bracketing Guidelines for Penn Korean TreeBank

This document describes the syntactic bracketing guidelines for the Penn Korean Treebank, which is an online corpus of Korean texts annotated with morphological and syntactic information. The corpus consists of around 54,000 words and 5,000 sentences. The Treebank uses a phrase structure style of annotation, making head/phrasal node distinctions, argument/adjunct distinctions, and identifying empty arguments and traces for moved constituents. This document is organized as follows. In section 2, the basic syntactic ingredients of a clause structure are presented. Some notational conventions are introduced in section 3, including different types of syntactic tags, such as head level tags, phrase level tags and function tags used in the Treebank. In section 4, the bracketing guidelines for various types of clauses are discussed, including simple clauses, subordinate clauses, and clauses with coordination. Several types of subcategorizaion frames found in the Treebank are then presented in section 5, followed by bracketing guidelines for various linguistic phenomena in sections 6 to 21, including guidelines for annotating punctuation. The document ends with guidelines for handling some bracketing ambiguities and for handling some confusing examples

Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer

Background Metastasis of breast cancer to distal organs is fatal. However, few studies have identified biomarkers that are associated with distant metastatic breast cancer. Furthermore, the inability of current biomarkers, such as HER2, ER, and PR, to differentiate between distant and nondistant metastatic breast cancers accurately has necessitated the development of novel biomarker candidates. Methods An integrated proteomics approach that combined filter-aided sample preparation, tandem mass tag labeling (TMT), high pH fractionation, and high-resolution MS was applied to acquire in-depth proteomic data from FFPE distant metastatic breast cancer tissues. A bioinformatics analysis was performed with regard to gene ontology and signaling pathways using differentially expressed proteins (DEPs) to examine the molecular characteristics of distant metastatic breast cancer. In addition, real-time polymerase chain reaction (RT-PCR) and invasion/migration assays were performed to validate the differential regulation and function of our protein targets. Results A total of 9441 and 8746 proteins were identified from the pooled and individual sample sets, respectively. Based on our criteria, TUBB2A was selected as a novel biomarker candidate. The metastatic activities of TUBB2A were subsequently validated. In our bioinformatics analysis using DEPs, we characterized the overall molecular features of distant metastasis and measured differences in the molecular functions of distant metastatic breast cancer between breast cancer subtypes. Conclusions Our report is the first study to examine the distant metastatic breast cancer proteome using FFPE tissues. The depth of our dataset allowed us to discover a novel biomarker candidate and a proteomic characteristics of distant metastatic breast cancer. Distinct molecular features of various breast cancer subtypes were also established. Our proteomic data constitute a valuable resource for research on distant metastatic breast cancer.This work was supported by the Industrial Strategic Technology Development Program (#10079271 and #20000134), funded by the Ministry of Trade, Industry, and Energy (MOTIE, Korea); the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (Grant Number: HI17C0048); the Basic Science Research Program through the Seoul National University Hospital Research Fund (26-2016-0020); and the National Research Foundation of Korea (NRF), funded by the Ministry of Science, ICT & Future Planning (Grant Number: 2018R1A1A1A05077484)

Mitochondrial-Targeting Anticancer Agent Conjugates and Nanocarrier Systems for Cancer Treatment

The mitochondrion is an important intracellular organelle for drug targeting due to its key roles and functions in cellular proliferation and death. In the last few decades, several studies have revealed mitochondrial functions, attracting the focus of many researchers to work in this field over nuclear targeting. Mitochondrial targeting was initiated in 1995 with a triphenylphosphonium-thiobutyl conjugate as an antioxidant agent. The major driving force for mitochondrial targeting in cancer cells is the higher mitochondrial membrane potential compared with that of the cytosol, which allows some molecules to selectively target mitochondria. In this review, we discuss mitochondria-targeting ligand-conjugated anticancer agents and their in vitro and in vivo behaviors. In addition, we describe a mitochondria-targeting nanocarrier system for anticancer drug delivery. As previously reported, several agents have been known to have mitochondrial targeting potential; however, they are not sufficient for direct application for cancer therapy. Thus, many studies have focused on direct conjugation of targeting ligands to therapeutic agents to improve their efficacy. There are many variables for optimal mitochondria-targeted agent development, such as choosing a correct targeting ligand and linker. However, using the nanocarrier system could solve some issues related to solubility and selectivity. Thus, this review focuses on mitochondria-targeting drug conjugates and mitochondria-targeted nanocarrier systems for anticancer agent delivery

Information-signal-transfer rate and energy loss in coupled vortex-state networks

We employed analytical and micromagnetic numerical calculations to elucidate coupled-vortexg-yration-enabled information-signal transfer and the related energy attenuation between vortex-state nanodisks. Specifically, we explored the vortex-gyration transfer rate and the energy attenuation coefficient in terms of the material parameters and dimensions of the coupled disks. Both the micromagnetic simulation and analytical results indicated that the transfer rate is determined by the relative polarization configuration, the saturation magnetization M-s, the radius (R)-to-thickness (L) ratio (R/L) of the given magnetic disks, and the interdistance, whereas the energy attenuation is governed by the intrinsic damping constant as well as the values of M-s, L, and R of the single disks. This work provides a foundation for manipulation of the technologically essential parameters in signal processing, namely speed and energy loss, based on coupled vortex-state networks.close5

Characteristics of Calcium Phosphate Films Prepared by Pulsed Laser Deposition under Various Water Vapor Pressures

Calcium phosphate films were prepared by using a pulsed laser deposition (PLD) technique with a KrF excimer laser (248 nm, 2 J/cm²) under a wide range of H2O pressures at a substrate temperature of 600℃. Sintered hydroxyapatite (HA) was used as the target. The background H2O pressure during deposition critically affected the density and the composition of the deposited films. With increasing H2O pressure, the growth rate increased, and the mass deposited was almost constant. Consequently, the density gradually decreased with H2O pressure, resulting in a porous microstructure under 0.37 Torr. The Ca/P ratio of the film decreased with H2O pressure, and the crystal structure of the deposited film changed in accordance with the Ca/P ratio. The observed peaks were from hydroxyapatite (Ca/P = 1.67) for H2O pressures above 0.13 Torr, and the peaks from high Ca/P phases, such as tetracalcium phosphate [Ca4O(PO4)2, Ca/P = 2] and CaO (Ca/P = ∞), were observed for the film deposited at 0.02 Torr. A high-density hydroxyapatite film with a high degree of crystallinity was obtained under a H2O pressure of 0.25 Torr

Influences of Ambient Gases on the Structure and the Composition of Calcium Phosphate Films Prepared by Pulsed Laser Deposition

Calcium phosphate films were prepared by using a pulsed KrF-laser deposition (PLD) method with a hydroxyapatite target in various ambient gases, such as Ar, O2 and H2O. The influence of the ambient gas on the properties of the deposited films was investigated. The chamber pressure and the substrate temperature were fixed at 0.25 Torr and 600℃, respectively. Calcium-rich amorphous calcium phosphate films were deposited with a low density in Ar due to the preferential resputtering of phosphorus from the growing film. In an O2 ambient, the density and the Ca/P ratio of the films were similar to those of the target. However, the deposited film was amorphous calcium phosphate and did not contain OH− groups. Polycrystalline hydroxyapatite films can be deposited in a H2O ambient because a sufficient supply of OH− groups from the ambient gas is essential for the growth of a hydroxyapatite film

Reversible Splenium Lesion of the Corpus Callosum in Hemorrhagic Fever with Renal Failure Syndrome

This is the first case of virus-associated encephalitis/encephalopathy in which the pathogen was Hantaan virus. A 53-yr-old man presented fever, renal failure and a hemorrhagic tendency and he was diagnosed with hemorrhagic fever with renal failure syndrome (HFRS). In the course of his illness, mild neurologic symptoms such as dizziness and confusion developed and magnetic resonance images revealed a reversible lesion in the splenium of the corpus callosum. This case suggests that HFRS patients with neurologic symptoms like dizziness and mental slowing should be considered to have structural brain lesions and to require brain imaging studies

FBXW7-mediated ERK3 degradation regulates the proliferation of lung cancer cells

Extracellular signal-regulated kinase 3 (ERK3) is an atypical member of the mitogen-activated protein kinase (MAPK) family, members of which play essential roles in diverse cellular processes during carcinogenesis, including cell proliferation, differentiation, migration, and invasion. Unlike other MAPKs, ERK3 is an unstable protein with a short half-life. Although deubiquitination of ERK3 has been suggested to regulate the activity, its ubiquitination has not been described in the literature. Here, we report that FBXW7 (F-box and WD repeat domain-containing 7) acts as a ubiquitination E3 ligase for ERK3. Mammalian two-hybrid assay and immunoprecipitation results demonstrated that ERK3 is a novel binding partner of FBXW7. Furthermore, complex formation between ERK3 and the S-phase kinase-associated protein 1 (SKP1)-cullin 1-F-box protein (SCF) E3 ligase resulted in the destabilization of ERK3 via a ubiquitination-mediated proteasomal degradation pathway, and FBXW7 depletion restored ERK3 protein levels by inhibiting this ubiquitination. The interaction between ERK3 and FBXW7 was driven by binding between the C34D of ERK3, especially at Thr417 and Thr421, and the WD40 domain of FBXW7. A double mutant of ERK3 (Thr417 and Thr421 to alanine) abrogated FBXW7-mediated ubiquitination. Importantly, ERK3 knockdown inhibited the proliferation of lung cancer cells by regulating the G1/S-phase transition of the cell cycle. These results show that FBXW7-mediated ERK3 destabilization suppresses lung cancer cell proliferation in vitro