High-throughput peptide quantification using mTRAQ reagent triplex

<p>Abstract</p> <p>Background</p> <p>Protein quantification is an essential step in many proteomics experiments. A number of labeling approaches have been proposed and adopted in mass spectrometry (MS) based relative quantification. The mTRAQ, one of the stable isotope labeling methods, is amine-specific and available in triplex format, so that the sample throughput could be doubled when compared with duplex reagents.</p> <p>Methods and results</p> <p>Here we propose a novel data analysis algorithm for peptide quantification in triplex mTRAQ experiments. It improved the accuracy of quantification in two features. First, it identified and separated triplex isotopic clusters of a peptide in each full MS scan. We designed a schematic model of triplex overlapping isotopic clusters, and separated triplex isotopic clusters by solving cubic equations, which are deduced from the schematic model. Second, it automatically determined the elution areas of peptides. Some peptides have similar atomic masses and elution times, so their elution areas can have overlaps. Our algorithm successfully identified the overlaps and found accurate elution areas. We validated our algorithm using standard protein mixture experiments.</p> <p>Conclusions</p> <p>We showed that our algorithm was able to accurately quantify peptides in triplex mTRAQ experiments. Its software implementation is compatible with Trans-Proteomic Pipeline (TPP), and thus enables high-throughput analysis of proteomics data.</p

In-Process Cutting Temperature Monitoring Method Based on Impedance Model of Dielectric Coating Layer at Tool-Chip Interface

This paper introduces a novel approach to in-process monitoring of the cutting temperature at the tool-chip interface (TCI). Currently, there are no tools available in the commercial market for measuring and monitoring cutting processes at the TCI region. Therefore, most of the studies about evaluating cutting temperature rely on simulation results without knowing the true temperature at the actual TCI region. In addition, recent cutting temperature measurement techniques have measurement errors occurring resulting from difficulty in estimations at the TCI region. However, the proposed method enables the measuring of cutting temperature by directly probing the localized TCI using a cutting tool coated with dielectric material. The study was conducted by utilizing the impedance characteristics of the dielectric outer layer of the cutting tool. A chemical vapor deposition (CVD) diamond coated insert that is commercially available was considered for the study to avoid wear effect. Impedance response of the dielectric layer under varying temperature conditions is assessed by Nyquist diagram using an impedance analyzer. The result of the Nyquist diagram showed temperature-dependent impedance characteristics that showed good agreement with the results from the thermal experiment which was a comparison between impedance response and elevated temperature. The impedance at the TCI for monitoring cutting temperature is measured under a turning process on a lathe using a constant current source. The impedance responses showed a significant decrease in impedance under various machining conditions which indicates a rise in cutting temperature. Moreover, different machining conditions showed different temperature profiles. The impedance responses were further characterized for depth of contact, which found that a drop in impedance corresponded to an increase in depth of contact. Therefore, the study showed that in-process monitoring of the cutting temperature is possible using an impedance model of the dielectric coating layer at the local TCI. Furthermore, with its versatility, this method is expected to measure the vibration, chatters, cutting force, and so on, as the results showed that impedance is not only sensitive to temperature but also to contact area. The application and expectation of this study is to provide real-time machining data to help end users in manufacturing industry to improve product quality, productivity, and prolonged lifespan of cutting tools

Prediction of velocity and attitude of a yacht sailing upwind by computational fluid dynamics

One of the most important factors in sailing yacht design is accurate velocity prediction. Velocity prediction programs (VPP's) are widely used to predict velocity of sailing yachts. VPP's, which are primarily based on experimental data and experience of long years, however suffer limitations when applied in realistic conditions. Thus, in the present study, a high fidelity velocity prediction method using computational fluid dynamics (CFD) was proposed. Using the developed method, velocity and attitude of a 30 feet sloop yacht, which was developed by Korea Research Institute of Ship and Ocean (KRISO) and termed KORDY30, were predicted in upwind sailing condition

Regioselective Construction and Screening of 1,3-Disubstituted Tetrahydroindazolones in Enantiomerically Pure Pairs

In this paper, we describe a regioselective synthetic pathway for enantiopure 1,3-disubstituted tetrahydroindazolone derivatives via the condensation of 2-acylcyclohexane-1,3-dione with various alkyl- and arylhydrazines using the steric effects of a Boc-protected pyrrolidine ring. This synthetic method has a broad scope for substrate generality for various hydrazines with excellent regioselectivity. To maximize the molecular diversity, further diversifications of 1,3-disubstituted tetrahydroindazolones were pursued by systematic <i>N</i>-modification of the secondary amine of the pyrrolidine ring using solution-phase parallel synthesis with polymer-supported reagents. A library containing a total of 272 drug-like tetrahydroindazolones, including 85 enantiomeric pairs, was constructed; the average purity, without further purification, was 95%

Ion-Driven Electrochemical Random-Access Memory-Based Synaptic Devices for Neuromorphic Computing Systems: A Mini-Review

To enhance the computing efficiency in a neuromorphic architecture, it is important to develop suitable memory devices that can emulate the role of biological synapses. More specifically, not only are multiple conductance states needed to be achieved in the memory but each state is also analogously adjusted by consecutive identical pulses. Recently, electrochemical random-access memory (ECRAM) has been dedicatedly designed to realize the desired synaptic characteristics. Electric-field-driven ion motion through various electrolytes enables the conductance of the ECRAM to be analogously modulated, resulting in a linear and symmetric response. Therefore, the aim of this study is to review recent advances in ECRAM technology from the material and device engineering perspectives. Since controllable mobile ions play an important role in achieving synaptic behavior, the prospect and challenges of ECRAM devices classified according to mobile ion species are discussed

Synthesis and Biological Evaluation of α‑Galactosylceramide Analogues with Heteroaromatic Rings and Varying Positions of a Phenyl Group in the Sphingosine Backbone

We designed and synthesized seven α-GalCer analogues with a pyrazole moiety and varying positions of a phenyl group in the sphingosine backbone to polarize cytokine secretion. On the basis of in vitro and in vivo biological evaluations, we found that analogue <b>5</b> induced greater polarization toward Th2 and greater secretion of the immunomodulatory cytokine, IL-4, over secretion of pro-inflammatory cytokines, IFN-γ and IL-17. Treatment of a single dose of analogue <b>5</b> markedly ameliorated disease pathogenesis in an animal model of an inflammatory demyelinating disease of the central nervous system, compared to that of KRN7000 (<b>1</b>). Therefore, this new α-GalCer analogue <b>5</b> is a novel iNKT ligand that stimulates the selective secretion of anti-inflammatory cytokines and regulates autoimmune diseases by reducing Th1 and Th17 responses