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Wang, Yuping

Publications and source records attributed to Wang, Yuping.

9 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

A filled function method for global optimization with inequality constraints

In this paper, we propose a new filled function method for finding a global minimizer of global optimization with inequality constraints. The proposed filled function is a continuously differentiable function with only one parameter. Then, we can use classical local optimization methods to find a better minimizer of the proposed filled function with a few parameter adjustment. The numerical experiments are made and the results show that the proposed filled function method is effective.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Mechanistic roles of microRNAs in hepatocarcinogenesis: A study of thioacetamide with multiple doses and time-points of rats

Environmental chemicals exposure is one of the primary factors for liver toxicity and hepatocarcinoma. Thioacetamide (TAA) is a well-known hepatotoxicant and could be a liver carcinogen in humans. The discovery of early and sensitive microRNA (miRNA) biomarkers in liver injury and tumor progression could improve cancer diagnosis, prognosis, and management. To study this, we performed next generation sequencing of the livers of Sprague-Dawley rats treated with TAA at three doses (4.5, 15 and 45 mg/kg) and four time points (3-, 7-, 14- and 28-days). Overall, 330 unique differentially expressed miRNAs (DEMs) were identified in the entire TAA-treatment course. Of these, 129 DEMs were found significantly enriched for the “liver cancer” annotation. These results were further complemented by pathway analysis (Molecular Mechanisms of Cancer, p53-, TGF-β-, MAPK- and Wnt-signaling). Two miRNAs (rno-miR-34a-5p and rno-miR-455-3p) out of 48 overlapping DEMs were identified to be early and sensitive biomarkers for TAA-induced hepatocarcinogenicity. We have shown significant regulatory associations between DEMs and TAA-induced liver carcinogenesis at an earlier stage than histopathological features. Most importantly, miR-34a-5p is the most suitable early and sensitive biomarker for TAA-induced hepatocarcinogenesis due to its consistent elevation during the entire treatment course.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

A novel procedure on next generation sequencing data analysis using text mining algorithm

Background: Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Methods: We report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure. Results: The output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data. Conclusion: The implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Supramolecular Gelation of Rigid Triangular Macrocycles through Rings of Multiple C–H$···$O Interactions Acting Cooperatively

When equimolar solutions of the enantiomeric naphthalenediimide-based highly rigid triangles $R-Δ$ and $S-Δ$ in ClCH 2 CH 2 Cl are mixed, the racemate $rac-Δ$ forms an organogel that is composed of interwoven fibers, resulting from the columnar stacking of the triangles in an alternating $R-Δ/S-Δ$ fashion. Under identical conditions, the pure enantiomers do not form organogels. Density functional theory calculations reveal that the racemic RS dimer is more stable than the RR dimer as a result of the enantiomeric relationship between $R-Δ$ and $S-Δ$, allowing them to act as two complementary rings comprised of 12 [C–H$···$O] interactions with an unprecedented and uninterrupted circular ADDAADDAADDA·DAADDAADDAAD alignment of hydrogen bond donors (D) and acceptors (A), in contrast with the square-wave manner in which the RR dimer forms a complementary yet interrupted ADADAD·DADADA circular sequence of six longer [C–H$···$O] hydrogen bonds. It follows that gelation is favored by weak interactions acting cooperatively in rings under precise stereoelectronic control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Synthesis and novel luminescence properties of one-dimension BaMoO{sub 4}:Ln{sup 3+} nanostructures

Highlights: • String BaMoO{sub 4}:Ln{sup 3+} nanobeans were prepared by a hydrothermal method. • The Decay dynamics were performed to study the photoluminescence of the BaMoO{sub 4}:Eu{sup 3+} nanobeans. • For BaMoO{sub 4}:Er{sup 3+}/Eu{sup 3+}, the {sup 2}P{sub 3/2} → {sup 4}I{sub 11/2} and {sup 2}H{sub 11/2}/{sup 4}S{sub 3/2} → {sup 4}I{sub 15/2} transitions were observed. - Abstract: String BaMoO{sub 4}:Ln{sup 3+} (Ln = Eu, Tb, Er, and Gd) nanobeans were prepared by a hydrothermal method. The samples were characterized by transmission electron microscope, scanning electron microscope, X-ray diffraction, X-ray photoelectron spectroscope, and Raman spectrometer. Under direct excitation in the charge transfer absorption band, concentration quenching phenomenon occurs and decay dynamics were performed to study the photoluminescence of the string BaMoO{sub 4}:Eu{sup 3+} nanobeans. In the emission spectra of BaMoO{sub 4}:Er{sup 3+}/Eu{sup 3+} under 274 nm excitation, the {sup 2}P{sub 3/2} → {sup 4}I{sub 11/2}, {sup 2}H{sub 11/2} → {sup 4}I{sub 15/2}, and {sup 4}S{sub 3/2} → {sup 4}I{sub 15/2} transitions from Er{sup 3+} ions were observed for the first time. In addition, the photoluminescence properties of BaMoO{sub 4}:Tb{sup 3+}/Eu{sup 3+} and BaMoO{sub 4}:Gd{sup 3+}/Eu{sup 3+} were also investigated.

36 MATERIALS SCIENCE↗
DOE OSTI2015

A seven-degree-of-freedom, time-dependent quantum dynamics study on the energy efficiency in surmounting the central energy barrier of the OH + CH{sub 3} → O + CH{sub 4} reaction

A time-dependent, quantum reaction dynamics calculation with seven degrees of freedom was carried out to study the energy efficiency in surmounting the approximate center energy barrier of OH + CH{sub 3}. The calculation shows the OH vibration excitations greatly enhance the reactivity, whereas the vibrational excitations of CH{sub 3} and the rotational excitations hinder the reactivity. On the basis of equal amount of total energy, although this reaction has a slight early barrier, it is the OH vibrational energy that is the dominate force in promoting the reactivity, not the translational energy. The studies on both the forward O + CH{sub 4} and reverse OH + CH{sub 3} reactions demonstrate, for these central barrier reactions, a small change of the barrier location can significantly change the energy efficacy roles on the reactivity. The calculated rate constants agree with the experimental data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Photoluminescence and photocatalytic activity of flowerlike hierarchical TiO{sub 2}:Sm{sup 3+} microspheres

Graphical abstract: Flowerlike hierarchical TiO{sub 2}:Sm{sup 3+} microspheres were successfully prepared via a solvothermal method. The crystalline size decreased with increasing Sm{sup 3+} concentration. Each TiO{sub 2}:Sm{sup 3+} microsphere consists of several dozen nanopetals, which are composed of several aggregated nanothorns. Under 290, 360, 362, and 368 nm excitation, the {sup 4}G{sub 5/2} → {sup 6}H{sub 5/2}, {sup 4}G{sub 5/2} → {sup 6}H{sub 7/2}, and {sup 4}G{sub 5/2} → {sup 6}H{sub 9/2} transitions were observed. The luminescence intensity increased with increasing Sm{sup 3+} concentration, up to about 1.5 mol%, and then decreased abruptly. In addition to the aforementioned photoluminescence properties, TiO{sub 2}:Sm{sup 3+} microspheres can present photocatalytic activity for the degradation of RhB. - Highlights: • Flowerlike hierarchical TiO{sub 2}:Sm{sup 3+} microspheres were synthesized by a solvothermal method. • TiO{sub 2}:Sm{sup 3+} microspheres can present photocatalytic activity for the degradation of RhB. • The optical properties of TiO{sub 2}:Sm{sup 3+} microspheres with different Sm{sup 3+} concentration were studied in detail. - Abstract: Flowerlike hierarchical TiO{sub 2}:Sm{sup 3+} microspheres were successfully prepared via a solvothermal method. The results of the X-ray diffraction measurements revealed that the TiO{sub 2}:Sm{sup 3+} microspheres were anatase phase. The crystalline size of microspheres decreased with increasing Sm{sup 3+} concentrations. Each TiO{sub 2}:Sm{sup 3+} microsphere consists of several dozen nanopetals, which are composed of several aggregated nanothorns. Under 290, 360, 362, and 368 nm excitation, the {sup 4}G{sub 5/2} → {sup 6}H{sub 5/2}, {sup 4}G{sub 5/2} → {sup 6}H{sub 7/2}, and {sup 4}G{sub 5/2} → {sup 6}H{sub 9/2} transitions were observed. The luminescence intensity increased with increasing Sm{sup 3+} concentration, up to about 1.5 mol%, and then decreased abruptly. The peak positions and the shape of emissions were independent of Sm{sup 3+} concentrations. In addition to the aforementioned photoluminescence properties, TiO{sub 2}:Sm{sup 3+} microspheres can possess superior photocatalytic activity for the degradation of RhB. In addition, the BET surface areas increased with increasing Sm{sup 3+} concentrations, which should be benefit for RhB adsorption.

36 MATERIALS SCIENCE↗