IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches

<p>Abstract</p> <p>Background</p> <p>One of the most promising aspects of metabolomics is metabolic modeling and simulation. Central to such applications is automated high-throughput identification and quantification of metabolites. NMR spectroscopy is a reproducible, nondestructive, and nonselective method that has served as the foundation of metabolomics studies. However, the automated high-throughput identification and quantification of metabolites in NMR spectroscopy is limited by severe spectral overlap. Although numerous software programs have been developed for resolving overlapping resonances, as well as for identifying and quantifying metabolites, most of these programs are frequency-domain methods, considerably influenced by phase shifts and baseline distortions, and effective only in small-scale studies. Almost all these programs require multiple spectra for each application, and do not automatically identify and quantify metabolites in batches.</p> <p>Results</p> <p>We created IQMNMR, an R package that integrates a relaxation algorithm, digital filter, and similarity search algorithm. It differs from existing software in that it is a time-domain method; it uses not only frequency to resolve overlapping resonances but also relaxation time constants; it requires only one NMR spectrum per application; is uninfluenced by phase shifts and baseline distortions; and most important, yields a batch of quantified metabolites.</p> <p>Conclusions</p> <p>IQMNMR provides a solution that can automatically identify and quantify metabolites by one-dimensional proton NMR spectroscopy. Its time-domain nature, stability against phase shifts and baseline distortions, requirement for only one NMR spectrum, and capability to output a batch of quantified metabolites are of considerable significance to metabolic modeling and simulation.</p> <p>IQMNMR is available at <url>http://cran.r-project.org/web/packages/IQMNMR/</url>.</p

Effect of Nano Tea Seed Oil Microcapsules on the Quality of Low Fat Minced Pork Products

Low-fat conversion of high-fat products met consumers' pursuit of health, and was one of the future development directions of meat products. In this study, the effects of two forms of tea seed oil (TSO) and nano tea seed oil microcapsules (NTM) on the physical and chemical properties of pork mince products were investigated, with no tea seed oil fat replacing pork mince as the control group. The water retention, cooking yield, water distribution, texture, microstructure, and fat oxidation level of different fat replacing pork mince products were studied. The results showed that the addition of 50% and 70% NTM could improve the water retention ability of pork minced meat products caused by TSO replacement. The T21 relaxation time and proportion of the NTM replacement group were not significantly different from those of the non-replacement control group (P>0.05), while the proportion of non-flowable water in the TSO replacement group was significantly decreased (P<0.05). The L* and b* values of the NTM replacement group were enhanced compared with those of the non-tea seed oil replacement group, and the a* value was decreased. Furthermore, the NTM replacement group had a significant effect on inhibiting fat oxidation, effectively prolonging the storage period. The microstructure results showed that the oil distribution in the NTM replacement group was more uniform than that in the TSO replacement group, and the oil was more closely bound to the protein. The texture characteristics results showed that TSO replacement would cause the deterioration of texture, while NTM could improve the deterioration. The elasticity and viscosity of pork minced meat with 70% NTM replacement were better than those of the 50% and 70% NTM replacement groups. In summary, the addition of 70% NTM can be evenly distributed in pork minced meat, and form more hydrogen bonds with proteins, so as to achieve the purpose of stabilizing the physical and chemical properties of low-fat pork minced meat, such as water retention, hardness, and elasticity. Therefore, the low-fat pork minced meat with 70% NTM is the best

MicroRNA-21 inhibitor sensitizes human glioblastoma cells U251 (PTEN-mutant) and LN229 (PTEN-wild type) to taxol

<p>Abstract</p> <p>Background</p> <p>Substantial data indicate that the oncogene microRNA 21 (miR-21) is significantly elevated in glioblastoma multiforme (GBM) and regulates multiple genes associated with cancer cell proliferation, apoptosis, and invasiveness. Thus, miR-21 can theoretically become a target to enhance the chemotherapeutic effect in cancer therapy. So far, the effect of downregulating miR-21 to enhance the chemotherapeutic effect to taxol has not been studied in human GBM.</p> <p>Methods</p> <p>Human glioblastoma U251 (PTEN-mutant) and LN229 (PTEN wild-type) cells were treated with taxol and the miR-21 inhibitor (in a poly (amidoamine) (PAMAM) dendrimer), alone or in combination. The 50% inhibitory concentration and cell viability were determined by the MTT assay. The mechanism between the miR-21 inhibitor and the anticancer drug taxol was analyzed using the Zheng-Jun Jin method. Annexin V/PI staining was performed, and apoptosis and the cell cycle were evaluated by flow cytometry analysis. Expression of miR-21 was investigated by RT-PCR, and western blotting was performed to evaluate malignancy related protein alteration.</p> <p>Results</p> <p>IC(50) values were dramatically decreased in cells treated with miR-21 inhibitor combine with taxol, to a greater extent than those treated with taxol alone. Furthermore, the miR-21 inhibitor significantly enhanced apoptosis in both U251 cells and LN229 cells, and cell invasiveness was obviously weakened. Interestingly, the above data suggested that in both the PTEN mutant and the wild-type GBM cells, miR-21 blockage increased the chemosensitivity to taxol. It is worth noting that the miR-21 inhibitor additively interacted with taxol on U251cells and synergistically on LN229 cells. Thus, the miR-21 inhibitor might interrupt the activity of EGFR pathways, independently of PTEN status. Meanwhile, the expression of STAT3 and p-STAT3 decreased to relatively low levels after miR-21 inhibitor and taxol treatment. The data strongly suggested that a regulatory loop between miR-21 and STAT3 might provide an insight into the mechanism of modulating EGFR/STAT3 signaling.</p> <p>Conclusions</p> <p>Taken together, the miR-21 inhibitor could enhance the chemo-sensitivity of human glioblastoma cells to taxol. A combination of miR-21 inhibitor and taxol could be an effective therapeutic strategy for controlling the growth of GBM by inhibiting STAT3 expression and phosphorylation.</p

Mid-infrared Self-Similar Pulse Compression in a Tapered Tellurite Photonic Crystal Fiber and Its Application in Supercontinuum Generation

In this paper, we design a tapered tellurite photonic crystal fiber (TTPCF) with nonlinear coefficient increasing along the propagation direction, and demonstrate the mid-infrared self-similar pulse compression of the fundamental soliton in such a TTPCF. When the variation of group-velocity dispersion, higher-order dispersion, higher-order nonlinearity, and linear loss are considered, a 1 ps pulse at wavelength 2.5 μm can be compressed to 62.16 fs after a 1.63-m long propagation, along with the negligible pedestal, compression factor Fc of 16.09, and quality factor Qc of 83.16%. Then the compressed pulse is launched into another uniform tellurite PCF designed, and highly coherent and octave-spanning supercontinuum (SC) is generated. Compared to the initial picosecond pulse, the compressed pulse has much larger tolerance of noise level for the SC generation. Our research results provide a promising solution to realize the fiber-based mid-infrared femtosecond pulse source for nonlinear photonics and spectroscopy

Mid-Infrared Self-Similar Pulse Compression in a Tapered Tellurite Photonic Crystal Fiber and Its Application in Supercontinuum Generation

In this paper, we design a tapered tellurite photonic crystal fiber (TTPCF) with nonlinear coefficient increasing along the propagation direction, and demonstrate the mid-infrared self-similar pulse compression of the fundamental soliton in such a TTPCF. When the variation of group-velocity dispersion, higher-order dispersion, higher-order nonlinearity, and linear loss are considered, a 1 ps pulse at wavelength 2.5 μm can be compressed to 62.16 fs after a 1.63-m long propagation, along with the negligible pedestal, compression factor Fc of 16.09, and quality factor Qc of 83.16%. Then the compressed pulse is launched into another uniform tellurite PCF, where highly coherent and octave-spanning supercontinuum (SC) is generated. Compared to the initial picosecond pulse, the compressed pulse has much larger tolerance of noise level for the SC generation. Our research results provide a promising solution to realize the fiber-based mid-infrared femtosecond pulse source for nonlinear photonics and spectroscopy

Self-similar Pcosecond Pulse Compression for Supercontinuum Generation at Mid-infrared Wavelength in Silicon Strip Waveguides

Self-similar pulse compression has important application in highly coherent supercontinuum (SC) generation. In this paper, we numerically present the mid-infrared self-similar picosecond pulse compression in a tapered suspended silicon strip waveguide, which is designed with exponentially decreasing dispersion profile along the direction of propagation. When the variation of the Kerr nonlinear coefficient ��(z), linear and nonlinear losses, higher-order nonlinearity, and higher-order dispersion are taken into consideration, the simulation result shows that a 1 ps input pulse centered at wavelength 2.8 μm could be self-similarly compressed to 47.06 fs in a 3.9-cm waveguide taper, along with a compression factor ��c of 21.25, quality factor ��c of 0.78, and negligible pedestal. After that, the compressed pulse is launched into a uniform silicon strip waveguide, which is used for the generation of SC. We numerically demonstrate that the coherence of the generated SC by the compressed pulse can be significantly improved when compared to that generated directly by the picosecond pulse. The simulation results can be used to realize on-chip mid-infrared femtosecond light source and highly coherent supercontinuum, which can promote the development of on-chip nonlinear optic

High Degree Picosecond Pulse Compression in Chalcogenide-Silicon Slot Waveguide Taper

In this paper, we propose and design a chalcogenide (As2S3)-based slot waveguide taper with exponentially decreasing dispersion profile to realize high-degree pulse compression of low-power chirped solitons. Based on the waveguide taper designed, pulse compression of fundamental solitons, and chirped 2-soliton breather are both investigated numerically. With self-similar pulse compression scheme, a 1 ps input pulse is compressed to 81.5 fs in 6 cm propagation. By using 2-soliton breather pulses, a 1 ps chirped pulse is compressed to 80.3 fs in just 2.54 cm. This is the first demonstration of the feasibility of high-degree nonlinear pulse compression in As2S3-based slot waveguide taper

Advances in bioorganic molecules inspired degradation and surface modifications on Mg and its alloys

Mg alloys possess biodegradability, suitable mechanical properties, and biocompatibility, which make them possible to be used as biodegradable implants. However, the uncontrollable degradation of Mg alloys limits their general applications. In addition to the factors from the metallic materials themselves, like alloy compositions, heat treatment process and microstructure, some external factors, relating to the test/service environment, also affect the degradation rate of Mg alloys, such as inorganic salts, bioorganic small molecules, bioorganic macromolecules. The influence of bioorganic molecules on Mg corrosion and its protection has attracted more and more attentions. In this work, the cutting-edge advances in the influence of bioorganic molecules (i.e., protein, glucose, amino acids, vitamins and polypeptide) and their coupling effect on Mg degradation and the formation of protection coatings were reviewed. The research orientations of biomedical Mg alloys in exploring degradation mechanisms in vitro were proposed, and the impact of bioorganic molecules on the protective approaches were also explored

Comprehensive analysis of passive generation of parabolic similaritons in tapered hydrogenated amorphous silicon photonic wires

Parabolic pulses have important applications in both basic and applied sciences, such as high power optical amplification, optical communications, all-optical signal processing, etc. The generation of parabolic similaritons in tapered hydrogenated amorphous silicon photonic wires at telecom (λ~1550 nm) and mid-IR (λ≥2100 nm) wavelengths is demonstrated and analyzed. The self-similar theory of parabolic pulse generation in passive waveguides with increasing nonlinearity is presented. A generalized nonlinear Schrödinger equation is used to describe the coupled dynamics of optical field in the tapered hydrogenated amorphous silicon photonic wires with either decreasing dispersion or increasing nonlinearity. The impacts of length dependent higher-order effects, linear and nonlinear losses including two-photon absorption, and photongenerated free carriers, on the pulse evolutions are characterized. Numerical simulations show that initial Gaussian pulses will evolve into the parabolic pulses in the waveguide taper designed

Determination of band alignment in the single layer MoS2/WSe2 heterojunction

The emergence of transition metal dichalcogenides (TMDs) as 2D electronic materials has stimulated proposals of novel electronic and photonic devices based on TMD heterostructures. Here we report the determination of band offsets in TMD heterostructures by using microbeam X-ray photoelectron spectroscopy ({\mu}-XPS) and scanning tunneling microscopy/spectroscopy (STM/S). We determine a type-II alignment between $\textrm{MoS}_2$ and $\textrm{WSe}_2$ with a valence band offset (VBO) value of 0.83 eV and a conduction band offset (CBO) of 0.76 eV. First-principles calculations show that in this heterostructure with dissimilar chalcogen atoms, the electronic structures of $\textrm{WSe}_2$ and $\textrm{MoS}_2$ are well retained in their respective layers due to a weak interlayer coupling. Moreover, a VBO of 0.94 eV is obtained from density functional theory (DFT), consistent with the experimental determination.Comment: ^ These authors contributed equally. *Corresponding author E-mail: [email protected], [email protected] 20 pages, 4 figures in main tex