Fast implicit active contour model for inverse lithography.

We combine the ideas from level-set methods in computer vision and inverse imaging to derive a generalized active contour model for inverse lithography problems endowed with a locally implemented semi-implicit difference scheme. We introduce a cognitive analogy to move an initial guess of the interesting pattern contour by image-driven forces to the boundaries of the desired layout pattern. We develop an efficient semi-implicit numerical scheme implemented in the vicinity of the zero level-set and apply additive operator splitting (AOS) with respect to coordinate axes to solve consecutive one-dimensional linear systems of equations with the Thomas method. We demonstrate with simulation results that computation and convergence efficiency are jointly improved with reduced optimization dimensionality and a sufficient large step-size.

Transcriptomic analysis of chicken immune response to infection of different doses of Newcastle disease vaccine.

Newcastle disease virus (NDV) is a contagious poultry paramyxovirus, leading to substantial economic losses to the poultry industry. Here, RNA-seq was carried out to investigate the altered expression of immune-related genes in chicken thymus within 96 h in response to NDV infection. In NDV-infected chicken thymus tissues, comparative transcriptome analysis revealed 1386 differentially expressed genes (DEGs) at 24 h with 989 up- and 397 down-regulated genes, 728 DEGs at 48 h with 567 up- and 161 down-regulated genes, 1514 DEGs at 72 h with 1016 up- and 498 down-regulated genes, and 1196 DEGs at 96 h with 522 up- and 674 down-regulated genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these candidate targets mainly participate in biological processes or biochemical, metabolic and signal transduction processes. Notably, there is large enrichment in biological processes, cell components and metabolic processes, which may be related to NDV pathogenicity. In addition, the expression of five immune-related DEGs identified by RNA-seq was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Our results indicated that the expression levels of AvBD5, IL16, IL22 and IL18R1 were obviously up-regulated, and Il-18 expression was also changed, but not significantly, which play key roles in the defense against NDV. Overall, we identified several candidate targets that may be involved in the regulation of NDV infection, which provide new insights into the complicated regulatory mechanisms of virus-host interactions, and explore new strategies for protecting chickens against the virus.

Wavenumber synthesis approach to high-resolution wavenumber scanning interference using a mode-hoped laser.

A new method for the synthesis of wavenumber series before and after mode hopping is proposed for depth-resolved wavenumber scanning interferometry. The classical Fourier transform is not suitable for mode hopping; consequently, the wavenumber scanning range of diode lasers is rather narrow, reducing the depth resolution and measurement accuracy. We show that the discontinuity in wavenumber domain interferograms caused by mode hopping can be removed by introducing the phase compensation of the interference spectrum. Thus, the wavenumber series before and after mode hopping can be synthesized. Experiments and numerical simulations validate the proposed method, and the measurement error is within 5nm.

Highly sensitive, wide dynamic range displacement sensor combining chromatic confocal system and phase-sensitive spectral optical coherence tomography.

A displacement sensor with nanometer-sensitivity and a submillimeter dynamic range is proposed. It integrates a chromatic confocal system and phase-sensitive spectral optical coherence tomography (PhS-SOCT) into the fiber-based Michelson interferometer and codes interference and confocal signals with spectral multiplexing. A displacement is evaluated using depth-resolved phase information decoded from the interference signal, which is unwrapped based on the position information decoded from the confocal signal. A sensor system with a 0.102mm dynamic range was built to validate the method. The temperature induced sample surface displacement was measured with a root mean square error of 3.9nm.

Improvement of depth resolution in depth-resolved wavenumber-scanning interferometry using wavenumber-domain least-squares algorithm: comparison and experiment.

It is important to improve the depth resolution in depth-resolved wavenumber-scanning interferometry (DRWSI) owing to the limited range of wavenumber scanning. In this work, a new nonlinear iterative least-squares algorithm called the wavenumber-domain least-squares algorithm (WLSA) is proposed for evaluating the phase of DRWSI. The simulated and experimental results of the Fourier transform (FT), complex-number least-squares algorithm (CNLSA), eigenvalue-decomposition and least-squares algorithm (EDLSA), and WLSA were compared and analyzed. According to the results, the WLSA is less dependent on the initial values, and the depth resolution δz is approximately changed from δz to δz/6. Thus, the WLSA exhibits a better performance than the FT, CNLSA, and EDLSA.

Measurement of depth-resolved thermal deformation distribution using phase-contrast spectral optical coherence tomography.

An updated B-scan method is proposed for measuring the evolution of thermal deformation fields in polymers. In order to measure the distributions of out-of-plane deformation and normal strain field, phase-contrast spectral optical coherence tomography (PC-SOCT) was performed with the depth range and resolution of 4.3 mm and 10.7 µm, respectively, as thermal loads were applied to three different multilayer samples. The relation between temperature and material refractive index was predetermined before the measurement. After accounting for the refractive index, the thermal deformation fields in the polymer were obtained. The measured thermal expansion coefficient of silicone sealant was approximately equal to its reference value. This method allows correctly assessing the mechanical properties in semitransparent polymers.

Eigenvalue decomposition and least squares algorithm for depth resolution of wavenumber-scanning interferometry.

Depth resolution of depth-resolved interferometry evaluated by Fourier transform is limited by the range of phase shifting. A novel algorithm, the eigenvalue decomposition and least squares algorithm (EDLSA), is proposed. Experimental results obtained using depth-resolved wavenumber-scanning interferometry demonstrate that the EDLSA performs better than the Fourier transform and complex number least squares algorithm. Not requiring any a priori information, the algorithm can replace the Fourier transform in depth-resolved interferometry with improved depth resolution.

Improvement of the depth resolution in depth-resolved wavenumber-scanning interferometry using multiple uncorrelated wavenumber bands.

In this article, we provide a method to improve the depth resolution of wide-field depth-resolved wavenumber-scanning interferometry (DRWSI), because its depth resolution is limited by the range of the wavenumber scanning and mode hopping of the light source. An optical wedge is put into the optical path to measure the series of the wavenumber on time using a 2D spatial Fourier transform (FT) of the interferograms. Those uncorrelated multiple bands of the wavenumbers due to mode hopping of the diode laser can be synthesized into one band, to enlarge the range of the wavenumber scanning. A random-sampling FT is put forward to evaluate the distribution of frequencies and phases of the multiple surfaces measured. The benefit is that the depth resolution of the DRWSI is enhanced significantly with a higher signal-to-noise ratio. Because of its simplicity and practicability, this method broadens the way to employing multiple different lasers or lasers with mode hopping as the light sources in the DRWSI.

Processing of fluorescence lifetime image using modified phasor approach: homo-FRET from the acceptor.

As the hardware of FLIM technique becomes mature, the most important criterion for FLIM application is the correct interpretation of its data. In this research, first of all, a more orthogonal phasor approach, called as Modified Phasor Approach (MPA), is put forward. It is a way to calculate the lifetime of the complex fluorescent process, and a rule to measure how much the fluorescence process deviates from single exponential decay. Secondly, MPA is used to analysis the time-resolved fluorescence processes of the transfected CHO-K1 Cell lines expressing adenosine receptor A1R tagged by CYP and YFP, measured in the channel of the acceptor. The image of the fluorescence lifetime and the multiplication of the fluorescence lifetime and deviation from single exponential decay reveal the details of the Homo-FRET. In one word, MPA provides the physical meaning in its whole modified phasor space, and broadens the way for the application of the fluorescence lifetime imaging.

Global analysis of dynamic fluorescence anisotropy by a polarized phasor approach.

Recently, the graphical analysis of the fluorescence lifetime imaging using the phasor approach has been highlight, and a series of the reports have made it on the way for the applications by the nonprofessionals. In this paper, we put forward a similar theory validated by the experiments for the dynamic fluorescence anisotropy imaging. By subtracting the perpendicular component from the parallel one in the frequency-domain polarization measurement, we deduce a new analytical expression about the fluorescence joint time, and find that as much as the fluorophore is a single exponential decay and r∞ is equal to zero, △I(t) is a single exponential decay with the time constant X as well, and the center of its histograms is located on the semicircle in the polarized phasor plot. In the end, we conclude that the fluorescence joint time is the best parameter to weigh the fluorescence dynamics for the macromolecules.

Confocal detection of planar homogeneous and heterogeneous immunosorbent assays.

Optically sectioned detection of fluorescence immunoassays using a confocal microscope enables the creation of both homo- and heterogeneous planar format assays. We report a set assays requiring optically sectioned detection using a model system and analysis procedures for separating signals of a surface layer from an overlying solution. A model sandwich assay with human immunoglobulin G as the target antigen is created on a glass substrate. The prepared surfaces are exposed to antigen and a FITC-labeled secondary antibody. The resulting preparations are either read directly to provide a homogeneous assay or after wash steps, giving a heterogeneous assay. The simplicity of the object shapes arising from the planar format makes the decomposition of analyte signals from the thin film bound to the surface and overlayer straightforward. Measured response functions of the thin film and overlayer fit well to the Cauchy-Lorentz and cumulative Cauchy-Lorentz functions, respectively, enabling the film and overlayer to be separated. Under the conditions used, the detection limits for the homogeneous and heterogeneous forms of the assay are 2.2 and 5.5 ng/ml, respectively. Planar format, confocally read fluorescence assays enable wash-free detection of antigens and should be applicable to a wide range of assays involving surface-bound species.