Coupled-mode theory for periodic side-coupled microcavity and photonic crystal structures

We use a phenomenological Hamiltonian approach to derive a set of coupled mode equations that describe light propagation in waveguides that are periodically side-coupled to microcavities. The structure exhibits both Bragg gap and (polariton like) resonator gap in the dispersion relation. The origin and physical significance of the two types of gaps are discussed. The coupled-mode equations derived from the effective field formalism are valid deep within the Bragg gaps and resonator gaps.Comment: 13 pages, 6 figure

Electrical Characterization of Soil for In-Situ Measurement of Liquefaction Potential

A new method for characterizing the fundamental sand properties with electrical parameters is described. Correlations are established between the electrical parameters and relative density, Dr, cyclic stress ratio, τ/ σ\u270, and the parameter K2max. An electrical probe, used to measure the electrical parameters in situ, is described. Field measurements, taken with the probe at one of the 1906 San Francisco earthquake sites, indicate that this is a viable alternative for the in situ evaluation of liquefaction potential

eipy: An Open-Source Python Package for Multi-modal Data Integration using Heterogeneous Ensembles

In this paper, we introduce eipy--an open-source Python package for developing effective, multi-modal heterogeneous ensembles for classification. eipy simultaneously provides both a rigorous, and user-friendly framework for comparing and selecting the best-performing multi-modal data integration and predictive modeling methods by systematically evaluating their performance using nested cross-validation. The package is designed to leverage scikit-learn-like estimators as components to build multi-modal predictive models. An up-to-date user guide, including API reference and tutorials, for eipy is maintained at https://eipy.readthedocs.io . The main repository for this project can be found on GitHub at https://github.com/GauravPandeyLab/eipy

Flexible Functional Forms Bernstein Polynomials

Motivated by the economic theory of cost functions, bivariate Bernstein polynomials are considered for approximating shape-restricted functions that are continuous, non-negative, monotone non-decreasing, concave, and homogeneous of degree one. We show the explicit rates of convergence of our approximating polynomials for general functions. We prove some interesting properties of bivariate Bernstein polynomials, including bimonotonicity for concave functions. Moreover, using the classical results, global approximations for shape-restricted functions can be achieved. We also note that concavity violation by the bivariate Bernstein polynomials occurs when the underlying true function ishomogeneous of degree one. However, this violation diminishes as indicces get large.bivariate Bernstein polynomials, rate of convergence, functional forms, flexibility, cost functions

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.

Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups in supporting fibrogenesis has not been investigated in vivo. Here, we used single-cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of macrophages in bleomycin-induced lung fibrosis in mice. A novel computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes (SingleR) enabled the subclustering of macrophages and revealed a disease-associated subgroup with a transitional gene expression profile intermediate between monocyte-derived and alveolar macrophages. These CX3CR1+SiglecF+ transitional macrophages localized to the fibrotic niche and had a profibrotic effect in vivo. Human orthologs of genes expressed by the transitional macrophages were upregulated in samples from patients with idiopathic pulmonary fibrosis. Thus, we have identified a pathological subgroup of transitional macrophages that are required for the fibrotic response to injury

Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin

<p>Abstract</p> <p>Background</p> <p>It is known that the highly pathogenic avian influenza A virus H5N1 binds strongly and with high specificity to the avian-type receptor by its hemagglutinin surface protein. This specificity is normally a barrier to viral transmission from birds to humans. However, strains may emerge with mutated hemagglutinin, potentially changing the receptor binding preference from avian to human-type. This hypothesis has been proven correct, since viral isolates from Vietnam and Thailand have been found which have increased selectivity toward the human cell receptor. The change in binding preference is due to mutation, which can be computationally modelled. The aim of this study is to further explore whether computational simulation could be used as a prediction tool for host type selectivity in emerging variants.</p> <p>Results</p> <p>Molecular dynamics simulation was employed to study the interactions between receptor models and hemagglutinin proteins from H5N1 strains A/Duck/Singapore/3/97, mutated A/Duck/Singapore/3/97 (Q222L, G224S, Q222L/G224S), A/Thailand/1(KAN-1)/2004, and mutated A/Thailand/1(KAN-1)/2004 (L129V/A134V). The avian receptor was represented by Siaα(2,3)Gal substructure and human receptor by Siaα(2,6)Gal. The glycoside binding conformation was monitored throughout the simulations since high selectivity toward a particular host occurs when the sialoside bound with the near-optimized conformation.</p> <p>Conclusion</p> <p>The simulation results showed all hemagglutinin proteins used the same set of amino acid residues to bind with the glycoside; however, some mutations alter linkage preferences. Preference toward human-type receptors is associated with a positive torsion angle, while avian-type receptor preference is associated with a negative torsion angle. According to the conformation analysis of the bound receptors, we could predict the relative selectivity in accordance with <it>in vitro </it>experimental data when disaccharides receptor analogs were used.</p

Students’ perceived changes and benefits in a mandatory service learning course

2016-2017 > Academic research: refereed > Refereed conference paper201804_a bcmaVersion of RecordPublishe