Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network.

Decoding DNA methylation sites through nanopore sequencing has emerged as a cutting-edge technology in the field of DNA methylation research, as it enables direct sequencing of native DNA molecules without the need for prior enzymatic or chemical treatments. During nanopore sequencing, methylation modifications on DNA bases cause changes in electrical current intensity. Therefore, constructing deep neural network models to decode the electrical signals of nanopore sequencing has become a crucial step in methylation site identification.

A time series representation of protein sequences for similarity comparison.

Based on the physicochemical indexes of 20 amino acids and the Hungarian algorithm, each amino acid was mapped into a vector. And, the protein sequence can be represented as time series in eleven-dimensional space. In addition, the DTW algorithm was applied to calculate the distance between two time series to compare the similarities of protein sequences.

Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks.

Background: More and more evidence showed that long non-coding RNAs (lncRNAs) play important roles in the development and progression of human sophisticated diseases. Therefore, predicting human lncRNA-disease associations is a challenging and urgently task in bioinformatics to research of human sophisticated diseases.

Results: In the work, a global network-based computational framework called as LRWRHLDA were proposed which is a universal network-based method.

Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur.

Data from the SEER reports reveal that the occurrence rate of a cancer type generally follows a unimodal distribution over age, peaking at an age that is cancer-type specific and ranges from 30+ through 70+. Previous studies attribute such bell-shaped distributions to the reduced proliferative potential in senior years but fail to explain why some cancers have their occurrence peak at 30+ or 40+. We present a computational model to offer a new explanation to such distributions.

A Generalized Iterative Map for Analysis of Protein Sequences.

Aim And Objective: The similarities comparison of biological sequences is an important task in bioinformatics. The methods of the similarities comparison for biological sequences are divided into two classes: sequence alignment method and alignment-free method. The graphical representation of biological sequences is a kind of alignment-free method, which constitutes a tool for analyzing and visualizing the biological sequences.

Depth perception based 3D holograms enabled with polarization-independent metasurfaces.

Metasurfaces consist of dielectric nanobrick arrays with different dimensions in the long and short axes can be used to generate different phase delays, predicting a new way to manipulate an incident beam in the two orthogonal directions separately. Here we demonstrate the concept of depth perception based three-dimensional (3D) holograms with polarization-independent metasurfaces. 4-step dielectric metasurfaces-based fan-out optical elements and holograms operating at 658 nm were designed and simulated.

Theoretical study of polarization dependence of carrier-induced refractive index change of quantum dot.

The influences of dot material component, barrier material component, aspect ratio and carrier density on the refractive index changes of TE mode and TM mode of columnar quantum dot are analyzed, and a multiparameter adjustment method is proposed to realize low polarization dependence of refractive index change. Then the quantum dots with low polarization dependence of refractive index change (<1.5%) within C-band (1530 nm - 1565 nm) are designed, and it shows that quantum dots with different material parameters are anticipated to have similar characteristics of low polarization dependence.

Dual field-of-view step-zoom metalens.

A conventional optical zoom system is bulky, expensive, and complicated for real-time adjustment. Recent progress in metasurface research has provided a new solution to achieve innovative compact optical systems. In this Letter, we propose a highly integrated step-zoom lens with dual field of view (FOV) based on double-sided metasurfaces.

Comparative transcriptome analysis of the different tissues between the cultivated and wild tomato.

Although domesticated tomato is cultivated by wild tomato, there are a lot of differences between cultivated tomato and wild tomato, such as shape, physiological function and life history. Many studies show that wild tomato has better salt resistance and drought resistance. In addition to, domesticated tomato's fruit is bigger and has more nutritious than wild tomato.

A Novel Protein Characterization Based on Pseudo Amino Acids Composition and Star-Like Graph Topological Indices.

Background And Objective: The rapidly growing number of protein data available creates necessity of computational methods with low complexity to infer accurate protein structure, function, and evolution.

Method: A new description of proteins based on five topological indices of star-like graph representation and the occurrence frequency of 20 amino acids was proposed to compare the similarities of proteins.

Results: A phylogenetic tree of eight ND6 proteins was constructed to demonstrate the effectiveness and rationality of our approach.

Ultracompact high-efficiency polarising beam splitter based on silicon nanobrick arrays.

Since the transmission of anisotropic nano-structures is sensitive to the polarisation of an incident beam, a novel polarising beam splitter (PBS) based on silicon nanobrick arrays is proposed. With careful design of such structures, an incident beam with polarisation direction aligned with the long axis of the nanobrick is almost totally reflected (~98.5%), whilst that along the short axis is nearly totally transmitted (~94.

A multiple information fusion method for predicting subcellular locations of two different types of bacterial protein simultaneously.

Subcellular localization prediction of bacterial protein is an important component of bioinformatics, which has great importance for drug design and other applications. For the prediction of protein subcellular localization, as we all know, lots of computational tools have been developed in the recent decades. In this study, we firstly introduce three kinds of protein sequences encoding schemes: physicochemical-based, evolutionary-based, and GO-based.

All-silicon nanorod-based Dammann gratings.

Established diffractive optical elements (DOEs), such as Dammann gratings, whose phase profile is controlled by etching different depths into a transparent dielectric substrate, suffer from a contradiction between the complexity of fabrication procedures and the performance of such gratings. In this Letter, we combine the concept of geometric phase and phase modulation in depth, and prove by theoretical analysis and numerical simulation that nanorod arrays etched on a silicon substrate have a characteristic of strong polarization conversion between two circularly polarized states and can act as a highly efficient half-wave plate. More importantly, only by changing the orientation angles of each nanorod can the arrays control the phase of a circularly polarized light, cell by cell.

Novel numerical characterization of protein sequences based on individual amino acid and its application.

The hydrophobicity and hydrophilicity of amino acids play a very important role in protein folding and its interaction with the environment and other molecules, as well as its catalytic mechanism. Based on the two physicochemical indexes, a 2D graphical representation of protein sequences is introduced; meanwhile, a new numerical characteristic has been proposed to compute the distance of different sequences for analysis of sequence similarity/dissimilarity on the basis of this graphical representation. Furthermore, we apply the new distance in the similarities/dissimilarities of ND5 proteins of nine species and predict the four major classes based on the dataset containing 639 domains.

Prediction of success for polymerase chain reactions using the Markov maximal order model and support vector machine.

Polymerase chain reaction (PCR) is hailed as one of the monumental scientific techniques of the twentieth century, and has become a common and often indispensable technique in many areas. However, researchers still frequently find some DNA templates very hard to amplify with PCR, although many kinds of endeavors were introduced to optimize the amplification. In fact, during the past decades, the experimental procedure of PCR was always the focus of attention, while the analysis of a DNA template, the PCR experimental subject itself, was almost neglected.

Theoretical study of polarization insensitivity of carrier-induced refractive index change of multiple quantum well.

Characteristics of polarization insensitivity of carrier-induced refractive index change of 1.55 μm tensile-strained multiple quantum well (MQW) are theoretically investigated. A comprehensive MQW model is proposed to effectively extend the application range of previous models.

Phylogenetic analysis of H7N9 avian influenza virus based on a novel mathematical descriptor.

A new mathematical descriptor was proposed based on 3D graphical representation. Using the method, we construct the phylogenetic trees of nine proteins of H7N9 influenza virus to analyze the originated source of H7N9. The results show that the evolution route of H7N9 avian influenza is from America through Europe to Asia.

Similarity/Dissimilarity analysis of protein sequences based on a new spectrum-like graphical representation.

Sequence comparison is one of the foundations in bioinformatics, which can be used to study evolutionary relations among the sequences. In this study, a 2D spectrum-like graphical representation of protein sequences is presented based on the hydrophobicity scale of amino acids. The frequencies of amplitudes of 4-subsequences are adopted to characterize a spectrum-like graph, and a 17D vector is used as the descriptor of protein sequence.

A novel descriptor of protein sequences and its application.

In this paper, a dynamic 3-D graphical representation of protein sequences is introduced based on three physical-chemical properties of amino acids. The coordinates of the graph have direct biological significance, which could reflect the innate structure of the proteins. The information of principal moments of inertia and range of axis coordinate are extracted as a novel mixed descriptor and proposed for the comparison of protein primary sequences.

A 3D graphical representation of protein sequences based on the Gray code.

Based on the order of 6-bit binary Gray code, a cyclic order of 20 amino acids is introduced. A novel 3D graphical representation of protein sequences is proposed according to the CGR of DNA sequences. Furthermore, the mathematical descriptor is suggested to characterize the graphical representation curve.

The graphical representation of protein sequences based on the physicochemical properties and its applications.

Based on the chaos game representation, a 2D graphical representation of protein sequences was introduced in which the 20 amino acids are rearranged in a cyclic order according to their physicochemical properties. The Euclidean distances between the corresponding amino acids from the 2-D graphical representations are computed to find matching (or conserved) fragments of amino acids between the two proteins. Again, the cumulative distance of the 2D-graphical representations is defined to compare the similarity of protein.

Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation.

A (two-dimensional) 2D graphical representation of protein sequences based on six physicochemical properties of amino acids is outlined. The numerical characterization of protein graphs is given as descriptors of protein sequences. It is not only useful for comparative study of proteins but also for encoding innate information about the structure of proteins.

Analysis of similarity/dissimilarity of protein sequences.

On the basis of a selected pair of physicochemical properties of amino acids, we introduce a dynamic 2D graphical representation of protein sequences. Then, we introduce and compare two numerical characterizations of protein graphs as descriptors to analyze the nine ND5 proteins. The approach is simple, convenient, and fast.