Applications of microwave-assisted proteomics in biotechnology

Biotechnology has recently celebrated 30 years both as a science and as a multi-billion dollar industry. One application of biotechnology is to use human genetic information to discover, develop, manufacture, and commercialize biotherapeutics. Recombinant proteins can be produced in large quantities at high purity. High-throughput proteomic analysis is at the heart of the biotechnology research and development process, and the industry is constantly striving to streamline and automate the analytical processes involved. Microwave-assisted proteomics has recently emerged as a tool for increasing the bio-catalysis of several processes including tryptic digestions lipase selectivities, identification of metal-catalyzed oxidation sites on proteins, identification of protein N- and C-termini and enzyme catalyzed N-linked deglycosylation. Here, we explore the above mentioned methods, and describe our experiences evaluating microwave-technology for other common proteomic protocols including: removal of N-terminal pyroglutamyl for antibody characterization, beta elimination and Michael addition for identification of phosphorylation sites on recombinant proteins and enzyme mediated O-linked deglycosylation.     

SNPlexing the human Y-chromosome: a single-assay system for major haplogroup screening

SNPs are one of the main sources of DNA variation among humans. Their unique properties make them useful polymorphic markers for a wide range of fields, such as medicine, forensics, and population genetics. Although several high-throughput techniques have been (and are being) developed for the vast typing of SNPs in the medical context, population genetic studies involve the typing of few and select SNPs for targeted research. This results in SNPs having to be typed in multiple reactions, consuming large amounts of time and of DNA. In order to improve the current situation in the area of human Y-chromosome diversity studies, we decided to employ a system based on a multiplex oligo ligation assay/PCR (OLA/PCR) followed by CE to create a Y multiplex capable of distinguishing, in a single reaction, all the major haplogroups and as many subhaplogroups on the Y-chromosome phylogeny as possible. Our efforts resulted in the creation of a robust and accurate 35plex (35 SNPs in a single reaction) that when tested on 165 human DNA samples from different geographic areas, proved capable of assigning samples to their corresponding haplogroup.     

氢原子在镍台阶面上吸附、振动和表面扩散行为的理论研究

本文用对势方法研究了氢原子在Ni(510)台阶面上的吸附和振动, 计算结果与实验符合得很好。并考察了氢原子在Ni(997)台阶面上的吸附和扩散, 结果表明,台阶对下台面上扩散的氢原子开成捕获势阱, 对上台面扩散的氢原子形成反射势,这也很好地支持了实验结果。     

The convolution theorem and the Franck–Condon integral

The convolution theorem is used to evaluate the Franck–Condon integral. It is shown that this integral becomes the matrix element between two “squeezed” states. This enables one to evaluate the integral by using boson operators. In addition, a general method is developed to obtain integrals involving Hermite polynomials with a displaced argument. In particular, the two‐center matrix element _g〈m|f(x_e)|n〉_e, is obtained, where f(x_e)=exp(Dx+Fx_e). ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 11–15, 1999     

Method for Finding the Exact Effective Hamiltonian of Time‐Driven Quantum Systems

Time‐driven quantum systems are important in many different fields of physics as cold atoms, solid state, optics, etc. Many of their properties are encoded in the time evolution operator or the effective Hamiltonian. Finding these operators usually requires very complex calculations that often involve some approximations. To perform this task, a systematic scheme that can be cast in the form of a symbolic computational algorithm is presented. It is suitable for periodic and non‐periodic potentials and, for convoluted systems, can also be adapted to yield numerical solutions. The method exploits the structure of the associated Lie group and a decomposition of the evolution operator on each group generator. To illustrate the use of the method, five examples are provided: harmonic oscillator with time‐dependent frequency (Paul trap), modulated optical lattice, time‐driven quantum oscillator, a step‐wise driving of a free particle, and the non‐periodic Caldirola‐Kanai Hamiltonian. To the extent of the authors' knowledge, whereas the exact form of Paul trap's evolution operator is well known, its effective Hamiltonian was until now unknown. The remaining four examples accurately reproduce previous results.     

Effect of combined polymers on the loss of efficiency caused by mechanical degradation in drag reducing flows through straight tubes

The mechanical molecular degradation in drag reducing flows is a huge problem in the effort to improve the efficiency of drag reducers, which is clearly increased when a combination of materials is used. Here, we analyze mixtures of three kinds of water-soluble polymers: Poly (ethylene oxide) (PEO), Polyacrylamide (PAM), and Xanthan Gum (XG). Two kinds of mixtures are tested: (a) PAM and XG; (b) PEO and XG. The synergy between the polymers is clearly noticeable. The values of the drag reduction (DR) obtained by the polymer–polymer combination was larger than that observed for a single polymer in a solution with the same total concentration of the mixture. Our tests are conducted in straight tubes where the total pressure is fixed. The values of DR are computed step-by-step, as the total amount of solution pass through the system. In doing so, we carefully took into account the loss of efficiency caused by the turbulent flow in the straight tubes. It is quite clear that the degradation of the flexible polymers (PEO and PAM) is delayed in the mixtures. In other words, besides the increase in the DR, the flexible polymers are more resistant when in the presence of the rigid one (XG). Such observation is the main conclusion of this work.     

Measurement of the phase behaviour of the binary systems {carbon dioxide (CO2) + non-ionic surfactants (CiEOj)}

Solubility experiments of ethoxylates surfactants denoted as C_iEO_j (where C_i = hydrocarbon tail, EO_j = oxyethylene groups, i = 6 to 8 and j = 3 to 5) in sub- and supercritical carbon dioxide were carried out at different temperatures, pressures, and concentrations in a Cailletet apparatus as a representative model for dry cleaning system. For a variety of compositions, results are reported for binary systems within temperature and pressure ranges of (260 to 310) K and (2.0 to 10) MPa respectively. In each experiment, the surfactants reach equilibrium with carbon dioxide at different concentrations. The data show that with all the surfactants upon increasing concentration, the liquid–liquid (L–L) curve shifts to lower temperatures. Therefore, the one-phase solution gap is reduced in pressure and temperature at higher concentrations. When the length of the hydrocarbon tail remains constant and the ethoxylated chain is increased from three to five groups, the L–L curve once again shifts to lower temperatures and the two phases start earlier. This effect can be attributed to the higher surfactant’s polarity due to the increase in j. On the other hand, when the number of ethoxylated groups j remains constant and the length of the hydrocarbon tail is increased from six to eight carbon atoms, no significant shift in the L–L curve is observed. That signals the fact that the appearance of two phases is directly related to the number of ethoxylated group which determine the polarity of the molecule.     

FASSVid: Fast and Accurate Semantic Segmentation for Video Sequences

Most of the methods for real-time semantic segmentation do not take into account temporal information when working with video sequences. This is counter-intuitive in real-world scenarios where the main application of such methods is, precisely, being able to process frame sequences as quickly and accurately as possible. In this paper, we address this problem by exploiting the temporal information provided by previous frames of the video stream. Our method leverages a previous input frame as well as the previous output of the network to enhance the prediction accuracy of the current input frame. We develop a module that obtains feature maps rich in change information. Additionally, we incorporate the previous output of the network into all the decoder stages as a way of increasing the attention given to relevant features. Finally, to properly train and evaluate our methods, we introduce CityscapesVid, a dataset specifically designed to benchmark semantic video segmentation networks. Our proposed network, entitled FASSVid improves the mIoU accuracy performance over a standard non-sequential baseline model. Moreover, FASSVid obtains state-of-the-art inference speed and competitive mIoU results compared to other state-of-the-art lightweight networks, with significantly lower number of computations. Specifically, we obtain 71% of mIoU in our CityscapesVid dataset, running at 114.9 FPS on a single NVIDIA GTX 1080Ti and 31 FPS on the NVIDIA Jetson Nano embedded board with images of size 1024×2048 and 512×1024, respectively.     

Unique green chromatography method for the determination of serotonin receptor antagonist (Ondansetron hydrochloride) related substances in a liquid formulation,robustness by quality by design-based design of experiments approach

Serotonin receptor antagonist drug Ondansetron hydrochloride injectable formulation containing all related substances was identified and quantified by a single, simple, sensitive, eco-friendly, and green high-performance liquid chromatography method. The disseverment of all impurities was achieved with the Discovery Cyano (250 × 4.6) mm, 5 μm column. The gradient program was composed of pH 5.7 phosphate buffer as mobile phase A and acetonitrile as mobile phase B. The flow rate, column compartment temperature, and detection wavelengths were 0.9 mL/min, 30°C, and 216 nm, respectively. The method was validated as per current regulatory guidelines. The obtained %relative standard deviation for the precision results was between 0.55 and 2.72% for all impurities. The correlation coefficient values from the linearity experiment for impurities and analyte were more than 0.995. The accuracy results were obtained between 88.4 and 113.0% for all impurities. Both sample and standard solutions showed 24 h stability at benchtop and refrigerator conditions. All impurities and analytes met the specificity and mass balance for all forced degradation conditions. Quality-by-design-based design of experiments was utilized to establish the method's robustness. Method greenness was assessed by using the current advanced tool green analytical procedure index, National Environmental Methods Index, and analytical eco-scale.     

Semiclassical propagator of the Wigner function

Propagation of the Wigner function is studied on two levels of semiclassical propagation: one based on the Van Vleck propagator, the other on phase-space path integration. Leading quantum corrections to the classical Liouville propagator take the form of a time-dependent quantum spot. Its oscillatory structure depends on whether the underlying classical flow is elliptic or hyperbolic. It can be interpreted as the result of interference of a pair of classical trajectories, indicating how quantum coherences are to be propagated semiclassically in phase space. The phase-space path-integral approach allows for a finer resolution of the quantum spot in terms of Airy functions.