Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases

We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions and may constitute a proportion of the mechanisms by which genetic variations cause individual differences or diseases. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases

User Detection Performance Analysis for Grant-Free Uplink Transmission in Large-Scale Antenna Systems

In this paper, user detection performance of a grant-free uplink transmission in a large scale antenna system is analyzed, in which a general grant-free multiple access is considered as the system model and Zadoff-Chu sequence is used for the uplink pilot. The false alarm probabilities of various user detection schemes under the target detection probabilities are evaluated

Direct Profiling the Post-Translational Modification Codes of a Single Protein Immobilized on a Surface Using Cu-free Click Chemistry

Combinatorial post-translational modifications (PTMs), which can serve as dynamic molecular barcodes, have been proposed to regulate distinct protein functions. However, studies of combinatorial PTMs on single protein molecules have been hindered by a lack of suitable analytical methods. Here, we describe erasable single-molecule blotting (eSiMBlot) for combinatorial PTM profiling. This assay is performed in a highly multiplexed manner and leverages the benefits of covalent protein immobilization, cyclic probing with different antibodies, and single molecule fluorescence imaging. Especially, facile and efficient covalent immobilization on a surface using Cu-free click chemistry permits multiple rounds (>10) of antibody erasing/reprobing without loss of antigenicity. Moreover, cumulative detection of coregistered multiple data sets for immobilized single-epitope molecules, such as HA peptide, can be used to increase the antibody detection rate. Finally, eSiMBlot enables direct visualization and quantitative profiling of combinatorial PTM codes at the single-molecule level, as we demonstrate by revealing the novel phospho-codes of ligand-induced epidermal growth factor receptor. Thus, eSiMBlot provides an unprecedentedly simple, rapid, and versatile platform for analyzing the vast number of combinatorial PTMs in biological pathways. Copyright © 2018 American Chemical Societ

Plasmonic Terahertz Wave Detector Based on Silicon Field-Effect Transistors with Asymmetric Source and Drain Structures

In this paper, we present the validity and potential capacity of a modeling and simulation environment for the nonresonant plasmonic terahertz (THz) detector based on the silicon (Si) field-effect transistor (FET) with a technology computer-aided design (TCAD) platform. The nonresonant and "overdamped" plasma-wave behaviors have been modeled by introducing a quasi-plasma electron charge box as a two-dimensional electron gas (2DEG) in the channel region only around the source side of Si FETs. Based on the coupled nonresonant plasma-wave physics and continuity equation on the TCAD platform, the alternate-current (AC) signal as an incoming THz wave radiation successfully induced a direct-current (DC) drain-to-source output voltage as a detection signal in a sub-THz frequency regime under the asymmetric boundary conditions with a external capacitance between the gate and drain. The average propagation length and density of a quasi-plasma have been confirmed as around 100 nm and 1x10(19)/cm(3), respectively, through the transient simulation of Si FETs with the modulated 2DEG at 0.7 THz. We investigated the incoming radiation frequency dependencies on the characteristics of the plasmonic THz detector operating in sub-THz nonresonant regime by using the quasi-plasma modeling on TCAD platform. The simulated dependences of the photoresponse with quasi-plasma 2DEG modeling on the structural parameters such as gate length and dielectric thickness confirmed the operation principle of the nonresonant plasmonic THz detector in the Si PET structure. The proposed methodologies provide the physical design platform for developing novel plasmonic THz detectors operating in the nonresonant detection mode.open3

Ductile Fracture Simulation of Full-scale Circumferential Cracked Pipes: (II) Stainless Steel

AbstractThis paper reports ductile fracture simulation of full-scale circumferentially cracked pipes using finite element (FE) damage analysis. In the structural integrity, without experimental investigations or with few ones, it is not an easy task to properly evaluate the crack initiation and crack propagation of large-scale components with a crack-like defect. Unfortunately, from an economic perspective, performing experiments of large-scale components would be consequently unfavorable. For these reasons, ductile fracture simulation using FE damage analysis to predict crack behavior is one efficient way to replace the test procedures. In order to simulate ductile tearing of large-scale cracked pipes, element-size-dependent critical damage model based on the stress-modified fracture strain model is proposed. To evaluate fracture behavior of full-scale cracked pipes, tensile and C(T) specimens are calibrated by FE analysis technique. Tensile properties and fracture toughness of stainless steel at 288oC are taken from Battelle Pipe Fracture Encyclopedia. After calibrations, simulated results of the full-scale pipes with a circumferential crack are compared with test data to validate the proposed method

The Distribution Strategy Of A Representative Fair Trade Organization In Korea: The Case Of Beautiful Coffee

This case study analyzes the distribution strategy of Beautiful Coffee, a leading fair trade organization in Korea. Because of their focus on matters of public interest, fair trade organizations often face financial difficulties, and such difficulties can limit their growth and force them to pursue differentiated distribution strategies. The results indicate that Beautiful Coffee can serve as a good role model for fair trade organizations and have important practical implications for firms pursuing sustainable growth as a social enterprise

Serum 25-hydroxyvitamin D levels and risk of colorectal cancer:an age-stratified analysis

Background and aims: the role of circulating 25-hydroxyvitamin D (25(OH)D) in prevention of early-onset colorectal cancer (CRC) in young adults under 50 years is uncertain. We evaluated the age-stratified associations (&lt;50 vs. ≥50 years) :circulating 25(OH)D levels and the risk of CRC in a large sample of Korean adults.Methods: our cohort study included 236,382 participants (mean [standard deviation] age, 38.0 [9.0] years) who underwent a comprehensive health examination, including measurement of serum 25(OH)D levels. Serum 25(OH)D levels were categorized as follows: &lt;10, 10–20, and ≥20 ng/mL. CRC, along with the histologic subtype, site, and invasiveness was ascertained through linkage with the national cancer registry. Cox proportional hazard models were used to estimate hazard ratios (HRs; 95% confidence intervals [CIs]) for incident CRC according to the serum 25(OH)D status, with adjustment for potential confounders.Results: during the 1,393,741 person-years of follow-up (median, 6.5 years; interquartile range, 4.5–7.5 years), 341 participants developed CRC (incidence rate, 19.2 per 105 person-years). Among young individuals aged &lt;50 years, serum 25(OH)D levels were inversely associated with the risk of incident CRC with HRs (95% CIs) of 0.61 (0.43–0.86) and 0.41 (0.27–0.63) for 25(OH)D 10-19 and ≥20 ng/mL, respectively, with respect to the reference (&lt;10 ng/mL) (p for trend &lt;0.001, time-dependent model). Significant associations were evident for adenocarcinoma, colon cancer, and invasive cancers. For those aged ≥50 years, associations were similar, although slightly attenuated compared to younger individuals. Conclusions: serum 25(OH)D levels may have beneficial associations with the risk of developing CRC for both early-onset and late-onset disease. <br/

Association between prostate-specific antigen and serum testosterone:A systematic review and meta-analysis

Background Serum testosterone assays are an important tool in the clinical evaluation of a number of endocrine disorders including male hypogonadism. However, serum testosterone has a limited role in real clinical use due to its inaccuracy. We aimed to assess the association between prostate-specific antigen (PSA) and testosterone as well as the effects of various types of testosterone replacement therapy (TRT) for PSA level. Methods Two electronic databases were screened: PubMed (1966 through December 2018) and Cochrane Library (1993 through December 2018). The first strategy compared the overall increase in PSA following testosterone treatment compared with placebo. The second strategy analyzed the overall association between PSA and testosterone among the observational studies. Results In the first strategy, 22 articles were included in the final analysis. In the second strategy, 18 studies were included. Testosterone replacement therapy (TRT) showed a significant change in PSA level compared to that in the placebo group (mean difference [MD]: 0.13, 95% CI: 0.01-0.25, P = .04). Compared to placebo, only intramuscular (IM) TRT shows a significant change in PSA level group (MD: 0.16, 95% CI: 0.01-0.30, P = .04), as neither the oral nor topical type showed a significant change in PSA. In the second strategy analysis, there was no overall correlation found between PSA and testosterone (z = 0.04, 95% CI: -0.04 to 0.12, P = .04; r = 0.039). However, in the subgroup of non-BPH (benign prostate hyperplasia), a significant correlation between PSA and testosterone (z = 0.07, 95% CI: 0.01-0.13, P = .009; r = 0.089) was found. Conclusions We found that TRT, particularly IM TRT, significantly changed the PSA level compared with the placebo group. Furthermore, there was a significant correlation between PSA and testosterone in patients with non-BPH. According to these findings, we suggest the possibility of PSA as a surrogate marker of testosterone