A fast-Fourier-transform method of topography and interferometry is proposed. By computer processing of a noncontour type of fringe pattern, automatic discrimination is achieved between elevation and depression of the object or wave-front form, which has not been possible by the fringe-contour-generation techniques. The method has advantages over moire topography and conventional fringe-contour interferometry in both accuracy and sensitivity. Unlike fringe-scanning techniques, the method is easy to apply because it uses no moving components.

Fourier-transform method of fringe-pattern analysis for computer-based topography and interferometry

On robust estimation of the location parameter

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing technology, ChIP-seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP-chip. With the decreasing cost of sequencing, ChIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms.

/pdf/chip-seq-advantages-and-challenges-of-a-maturing-technology-57od1mnvrx.pdf

ChIP-Seq: advantages and challenges of a maturing technology

It is shown that the ordinary semiclassical theory of the absorption of light by exciton states is not completely satisfactory (in contrast to the case of absorption due to interband transitions). A more complete theory is developed. It is shown that excitons are approximate bosons, and, in interaction with the electromagnetic field, the exciton field plays the role of the classical polarization field. The eigenstates of the system of crystal and radiation field are mixtures of photons and excitons. The ordinary one-quantum optical lifetime of an excitation is infinite. Absorption occurs only when "three-body" processes are introduced. The theory includes "local field" effects, leading to the Lorentz local field correction when it is applicable. A Smakula equation for the oscillator strength in terms of the integrated absorption constant is derived.

a Quantum-Mechanical Theory of the Contribution of Excitons to the Complex Dielectric Constant of Crystals.

Motivation: Chromatin states are the key to gene regulation and cell identity. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) is increasingly being used to map epigenetic states across genomes of diverse species. Chromatin modification profiles are frequently noisy and diffuse, spanning regions ranging from several nucleosomes to large domains of multiple genes. Much of the early work on the identification of ChIP-enriched regions for ChIP-Seq data has focused on identifying localized regions, such as transcription factor binding sites. Bioinformatic tools to identify diffuse domains of ChIP-enriched regions have been lacking.

Results: Based on the biological observation that histone modifications tend to cluster to form domains, we present a method that identifies spatial clusters of signals unlikely to appear by chance. This method pools together enrichment information from neighboring nucleosomes to increase sensitivity and specificity. By using genomic-scale analysis, as well as the examination of loci with validated epigenetic states, we demonstrate that this method outperforms existing methods in the identification of ChIP-enriched signals for histone modification profiles. We demonstrate the application of this unbiased method in important issues in ChIP-Seq data analysis, such as data normalization for quantitative comparison of levels of epigenetic modifications across cell types and growth conditions.

Availability: http://home.gwu.edu/~wpeng/Software.htm 

Contact: [email protected]

Supplementary information:Supplementary data are available at Bioinformatics online.

/pdf/a-clustering-approach-for-identification-of-enriched-domains-20j4tro7tk.pdf

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

We performed scanning tunneling microscope (STM) studies to observe the surface electronic structure of the following semiconducting charge-transfer complexes: dipropylamine-tetracyanoquinodimethane [DPA(TCNQ)${}_{2}$], triethylammonium [TEA (TCNQ)${}_{2}$], and $N$-ethylmorpholinium [HEM(TCNQ)${}_{2}$], which all possess the molecularly flat $\mathit{bc}$ surface terminated predominately with the quasi-one-dimensional (1D) TCNQ${}^{\ensuremath{-}0.5}$ anion chains or the corresponding DPA${}^{+}$, TEA${}^{+}$, and HEM${}^{+}$ cations contributing a lesser fraction. On the $\mathit{bc}$ surfaces terminated with TCNQ${}^{\ensuremath{-}0.5}$ anions for all crystals, the $4{k}_{F}$[DPA(TCNQ)${}_{2}$] or $2{k}_{F}$ [TEA(TCNQ)${}_{2}$ and HEM(TCNQ)${}_{2}$] charge density wave (CDW) driven by the spin-Peierls or Peierls instability for the quasi-1D TCNQ${}^{\ensuremath{-}0.5}$ chains, respectively, which occur already within the bulk, were probed by use of STM on the crystal surfaces. In that the surface lattice constants obtained from CDW are in good agreement with the bulk ones obtained by x-ray diffraction, such CDWs are commensurate. This modulation of the electric structure is so distinct that the geometric corrugation of individual TCNQ anions was hardly traced during our STM measurements. On the $\mathit{bc}$ surfaces terminated with DPA${}^{+}$, TEA${}^{+}$, and HEM${}^{+}$ cations, the STM images with submolecular resolution represent the geometric corrugation of individual molecular cations, and the surface lattice constants obtained deviate greatly from that of the x-ray crystal structures, indicating self-reassembling of the surface cations.

Characteristics of charge density waves on the surfaces of quasi-one-dimensional charge-transfer complex layered organic crystals

Fine-grained human action recognition is a core research topic in computer vision. Inspired by the recently proposed hierarchy representation of fine-grained actions in FineGym and SlowFast network for action recognition, we propose a novel multi-task network which exploits the FineGym hierarchy representation to achieve effective joint learning and prediction for fine-grained human action recognition. The multi-task network consists of three pathways of SlowOnly networks with gradually increased frame rates for events, sets and elements of fine-grained actions, followed by our proposed integration layers for joint learning and prediction. It is a two-stage approach, where it first learns deep feature representation at each hierarchical level, and is followed by feature encoding and fusion for multi-task learning. Our empirical results on the FineGym dataset achieve a new state-of-the-art performance, with 91.80% Top-1 accuracy and 88.46% mean accuracy for element actions, which are 3.40% and 7.26% higher than the previous best results.

Joint Learning On The Hierarchy Representation for Fine-Grained Human Action Recognition

We demonstrate that a high-index dielectric Si metasurface with a designed chiral unit structure possesses an exceptional point (EP) when it is described by a non-Hermitian Hamiltonian associated with the transmission matrix. By encircling any path in the parameter space around the EP, topologically protected 2π-phase accumulation occurs. These typical non-Hermitian properties are ascribed to complex scattering phenomena related to the coupling between electric and magnetic dipolar modes from the high-index dielectric Si metasurface. The topologically guaranteed entire 2π-phase accumulation and chiral distinction around the EP open up many promising possibilities in nanophotonic device designing; for instance, phase-only and polarization multiplexing holograms are realized in this work.

https://pubs.acs.org/doi/pdf/10.1021/acsomega.2c04448

Study of a High-Index Dielectric Non-Hermitian Metasurface and Its Application in Holograms

A mattress assembly, comprising: substantially nonporous bottom and side walls forming a mattress foundation; a mattress inner core disposed in the mattress foundation being permeable to air; nonporous top cover covering the mattress inner core, the nonporous top cover having apertures at predetermined locations to allow the flow of air therethrough; and a fan disposed with the mattress assembly for forcing air into the mattress inner core whereby the air is forced out the top cover so as to reduce the accumulation of carbon dioxide in bedding on the top cover of the mattress.

Feng Lin

Papers

Characteristics of charge density waves on the surfaces of quasi-one-dimensional charge-transfer complex layered organic crystals

Joint Learning On The Hierarchy Representation for Fine-Grained Human Action Recognition

Study of a High-Index Dielectric Non-Hermitian Metasurface and Its Application in Holograms

Binary Plankton Image Classification Using Pairwise Classifiers.

Vessel intimal extraction of coronary optical coherence tomography imagery based on an improved CV model