A continuous wavelet transform algorithm for peak detection

Contactless conductivity detector technology has unique advantages for microfluidic applications. However, the low S/N and varying baseline makes the signal analysis difficult. In this paper, a continuous wavelet transform-based peak detection algorithm was developed for CE signals from microfluidic chips. The Ridger peak detection algorithm is based on the MassSpecWavelet algorithm by Du et al. [Bioinformatics 2006, 22, 2059-2065], and performs a continuous wavelet transform on data, using a wavelet proportional to the first derivative of a Gaussian function. It forms sequences of local maxima and minima in the continuous wavelet transform, before pairing sequences of maxima to minima to define peaks. The peak detection algorithm was tested against the Cromwell, MassSpecWavelet, and Linear Matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometer Peak Indication and Classification algorithms using experimental data. Its sensitivity to false discovery rate curve is superior to other techniques tested.     

Maximum spectrum of continuous wavelet transform and its application in resolving an overlapped signal

To estimate the number of peaks and to find the individual peak positions in an overlapped signal, a new method called maximum spectrum of continuous wavelet transform (MSCWT) was developed by extracting the maximum coefficients of continuous wavelet transform (CWT). The peak position in MSCWT was the same as that in its original signal. In this process, CWT was performed not on a single dilation but on an appreciation dilation range. To obtain such a range, a new criterion was introduced to choose a center dilation, which was used to form the dilation range. If Cdilation denoted the center dilation, the proper dilation range was [Cdilation -6 +/- 2, Cdilation +1 +/- 1]. The Mexican Hat function was an analytical wavelet. Utilizing the information of the peak number and the position detected by MSCWT, a fitting route was performed to recover the original signal. One simulated and four true overlapped signals, including high performance liquid chromatography (HPLC), ultraviolet-visible (UV) spectrum, and differential pulse voltammetric (DPV), were processed, and the results indicated that MSCWT could detect an overlapped peak number and position, and the curve fitting based on information of MSCWT had a higher accuracy. The proposed method was an efficient one in resolving different types of overlapped signals.     

Robust alignment of chromatograms by statistically analyzing the shifts matrix generated by moving window fast Fourier transform cross‐correlation

Retention time shift is one of the most challenging problems during the preprocessing of massive chromatographic datasets. Here, an improved version of the moving window fast Fourier transform cross‐correlation algorithm is presented to perform nonlinear and robust alignment of chromatograms by analyzing the shifts matrix generated by moving window procedure. The shifts matrix in retention time can be estimated by fast Fourier transform cross‐correlation with a moving window procedure. The refined shift of each scan point can be obtained by calculating the mode of corresponding column of the shifts matrix. This version is simple, but more effective and robust than the previously published moving window fast Fourier transform cross‐correlation method. It can handle nonlinear retention time shift robustly if proper window size has been selected. The window size is the only one parameter needed to adjust and optimize. The properties of the proposed method are investigated by comparison with the previous moving window fast Fourier transform cross‐correlation and recursive alignment by fast Fourier transform using chromatographic datasets. The pattern recognition results of a gas chromatography mass spectrometry dataset of metabolic syndrome can be improved significantly after preprocessing by this method. Furthermore, the proposed method is available as an open source package at https://github.com/zmzhang/MWFFT2 .     

2nd-order spline wavelet convolution method in resolving chemical overlapped peaks

A 2nd-order spline wavelet convolution method in resolving overlapped peaks is developed. It determines the number of peaks, peak positions and width through wavelet's convolution, then uses spline function to construct the resoluter, which is used to resolve overlapped peaks. Theoretical proof is given, and the selections of wavelets and parameters are discussed. It is proven that baseline separation can be achieved after processed, the relative errors of peak position and area are less than 0.2% and 4.0% respectively. It can be directly applied to seriously overlapped signals, noisy signals and multi-component signals, and the results are satisfactory. It is a novel effective method for resolution.     

DR2DI: a powerful computational tool for predicting novel drug-disease associations

Finding the new related candidate diseases for known drugs provides an effective method for fast-speed and low-risk drug development. However, experimental identification of drug-disease associations is expensive and time-consuming. This motivates the need for developing in silico computational methods that can infer true drug-disease pairs with high confidence. In this study, we presented a novel and powerful computational tool, DR2DI, for accurately uncovering the potential associations between drugs and diseases using high-dimensional and heterogeneous omics data as information sources. Based on a unified and extended similarity kernel framework, DR2DI inferred the unknown relationships between drugs and diseases using Regularized Kernel Classifier. Importantly, DR2DI employed a semi-supervised and global learning algorithm which can be applied to uncover the diseases (drugs) associated with known and novel drugs (diseases). In silico global validation experiments showed that DR2DI significantly outperforms recent two approaches for predicting drug-disease associations. Detailed case studies further demonstrated that the therapeutic indications and side effects of drugs predicted by DR2DI could be validated by existing database records and literature, suggesting that DR2DI can be served as a useful bioinformatic tool for identifying the potential drug-disease associations and guiding drug repositioning. Our software and comparison codes are freely available at https://github.com/huayu1111/DR2DI.     

Resolution of Overlapping Chromatographic Peaks Using a Genetic Algorithm

ABSTRACT

A genetic algorithm for resolution of overlapping chromatographic peaks (GAROCP) using real-number coding, non-uniform mutation and arithmetical crossover methods is described in this paper. It was applied to resolution of highly overlapped multicomponent high-performance liquid chromatographic peaks by fitting experimental chromatogram to the exponentially modified Gaussian (EMG) model. The genetic algorithm was used to find the minimum of fitting error to optimize the parameters in the EMG functions which determine the shape and area of each peak. The applicability of the method was investigated with both simulated signals calculated by EMG functions and experimental multicomponent overlapping chromatograms.     

Autopiquer - a Robust and Reliable Peak Detection Algorithm for Mass Spectrometry

We present a simple algorithm for robust and unsupervised peak detection by determining a noise threshold in isotopically resolved mass spectrometry data. Solving this problem will greatly reduce the subjective and time-consuming manual picking of mass spectral peaks and so will prove beneficial in many research applications. The Autopiquer approach uses autocorrelation to test for the presence of (isotopic) structure in overlapping windows across the spectrum. Within each window, a noise threshold is optimized to remove the most unstructured data, whilst keeping as much of the (isotopic) structure as possible. This algorithm has been successfully demonstrated for both peak detection and spectral compression on data from many different classes of mass spectrometer and for different sample types, and this approach should also be extendible to other types of data that contain regularly spaced discrete peaks.

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Effective single-cell clustering through ensemble feature selection and similarity measurements

Single-cell RNA sequencing technologies have revolutionized biomedical research by providing an effective means to profile gene expressions in individual cells. One of the first fundamental steps to perform the in-depth analysis of single-cell sequencing data is cell type classification and identification. Computational methods such as clustering algorithms have been utilized and gaining in popularity because they can save considerable resources and time for experimental validations. Although selecting the optimal features (i.e., genes) is an essential process to obtain accurate and reliable single-cell clustering results, the computational complexity and dropout events that can introduce zero-inflated noise make this process very challenging. In this paper, we propose an effective single-cell clustering algorithm based on the ensemble feature selection and similarity measurements. We initially identify the set of potential features, then measure the cell-to-cell similarity based on the subset of the potentials through multiple feature sampling approaches. We construct the ensemble network based on cell-to-cell similarity. Finally, we apply a network-based clustering algorithm to obtain single-cell clusters. We evaluate the performance of our proposed algorithm through multiple assessments in real-world single-cell RNA sequencing datasets with known cell types. The results show that our proposed algorithm can identify accurate and consistent single-cell clustering. Moreover, the proposed algorithm takes relative expression as input, so it can easily be adopted by existing analysis pipelines. The source code has been made publicly available at https://github.com/jeonglab/scCLUE.     

Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics

Native mass spectra of large, polydisperse biomolecules with repeated subunits, such as lipoprotein Nanodiscs, can often be challenging to analyze by conventional methods. The presence of tens of closely spaced, overlapping peaks in these mass spectra can make charge state, total mass, or subunit mass determinations difficult to measure by traditional methods. Recently, we introduced a Fourier Transform-based algorithm that can be used to deconvolve highly congested mass spectra for polydisperse ion populations with repeated subunits and facilitate identification of the charge states, subunit mass, charge-state-specific, and total mass distributions present in the ion population. Here, we extend this method by investigating the advantages of using overtone peaks in the Fourier spectrum, particularly for mass spectra with low signal-to-noise and poor resolution. This method is illustrated for lipoprotein Nanodisc mass spectra acquired on three common platforms, including the first reported native mass spectrum of empty “large” Nanodiscs assembled with MSP1E3D1 and over 300 noncovalently associated lipids. It is shown that overtone peaks contain nearly identical stoichiometry and charge state information to fundamental peaks but can be significantly better resolved, resulting in more reliable reconstruction of charge-state-specific mass spectra and peak width characterization. We further demonstrate how these parameters can be used to improve results from Bayesian spectral fitting algorithms, such as UniDec.

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PEPR: pipelines for evaluating prokaryotic references

The rapid adoption of microbial whole genome sequencing in public health, clinical testing, and forensic laboratories requires the use of validated measurement processes. Well-characterized, homogeneous, and stable microbial genomic reference materials can be used to evaluate measurement processes, improving confidence in microbial whole genome sequencing results. We have developed a reproducible and transparent bioinformatics tool, PEPR, Pipelines for Evaluating Prokaryotic References, for characterizing the reference genome of prokaryotic genomic materials. PEPR evaluates the quality, purity, and homogeneity of the reference material genome, and purity of the genomic material. The quality of the genome is evaluated using high coverage paired-end sequence data; coverage, paired-end read size and direction, as well as soft-clipping rates, are used to identify mis-assemblies. The homogeneity and purity of the material relative to the reference genome are characterized by comparing base calls from replicate datasets generated using multiple sequencing technologies. Genomic purity of the material is assessed by checking for DNA contaminants. We demonstrate the tool and its output using sequencing data while developing a Staphylococcus aureus candidate genomic reference material. PEPR is open source and available at https://github.com/usnistgov/pepr.     

Absolute configuration of Buagafuran:An experimental and theoretical electronic circular dichroism study

Buagafuran is a novel drug candidate derived from natural product.Its absolute configuration has been confirmed by electronic circular dichroism combined with modern quantum-chemical calculation using time-dependent density functional theory.The predicted UV absorbance peak is underestimated by several nanometers compared with the experimental data.The applicability of empirical rule for the C=C-C-O system in Buagafuran has also been discussed.Our results show that electronic circular dichroism could be a useful tool for the absolute configuration assignment of chiral drugs,especially for the oily or semisolid substances,whose crystal structures are impossible to obtain.     

Amyloid beta peptides electrochemistry: A review

Alzheimer disease is a progressive age-related neurodegenerative disorder estimated to affect up to 107 million people by 2050, its pathology is associated with the dysfunction of the amyloid beta (Aβ) peptide mechanism, among others. Electrochemical methods were successfully applied for Aβ electrochemical characterisation and have received increased attention in Aβ research. This review discusses the recent advances on the direct electrochemical detection of Aβ redox mechanisms, fibrilization and interaction with metal ions based on the electrochemical detection of the Aβ′s

,

and

amino acid residues oxidation peaks.     

Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates

The conversion of polymer parameterization from internal coordinates (bond lengths, angles, and torsions) to Cartesian coordinates is a fundamental task in molecular modeling, often performed using the natural extension reference frame (NeRF) algorithm. NeRF can be parallelized to process multiple polymers simultaneously, but is not parallelizable along the length of a single polymer. A mathematically equivalent algorithm, pNeRF, has been derived that is parallelizable along a polymer's length. Empirical analysis demonstrates an order-of-magnitude speed up using modern GPUs and CPUs. In machine learning-based workflows, in which partial derivatives are backpropagated through NeRF equations and neural network primitives, switching to pNeRF can reduce the fractional computational cost of coordinate conversion from over two-thirds to around 10%. An optimized TensorFlow-based implementation of pNeRF is available on GitHub at https://github.com/aqlaboratory/pnerf © 2018 Wiley Periodicals, Inc.     

DeepReac+: deep active learning for quantitative modeling of organic chemical reactions

Various computational methods have been developed for quantitative modeling of organic chemical reactions; however, the lack of universality as well as the requirement of large amounts of experimental data limit their broad applications. Here, we present DeepReac+, an efficient and universal computational framework for prediction of chemical reaction outcomes and identification of optimal reaction conditions based on deep active learning. Under this framework, DeepReac is designed as a graph-neural-network-based model, which directly takes 2D molecular structures as inputs and automatically adapts to different prediction tasks. In addition, carefully-designed active learning strategies are incorporated to substantially reduce the number of necessary experiments for model training. We demonstrate the universality and high efficiency of DeepReac+ by achieving the state-of-the-art results with a minimum of labeled data on three diverse chemical reaction datasets in several scenarios. Collectively, DeepReac+ has great potential and utility in the development of AI-aided chemical synthesis. DeepReac+ is freely accessible at https://github.com/bm2-lab/DeepReac.

Based on GNNs and active learning, DeepReac+ is designed as a universal framework for quantitative modeling of chemical reactions. It takes molecular structures as inputs directly and adapts to various prediction tasks with fewer training data.     

Azahar: a PyMOL plugin for construction,visualization and analysis of glycan molecules

Glycans are key molecules in many physiological and pathological processes. As with other molecules, like proteins, visualization of the 3D structures of glycans adds valuable information for understanding their biological function. Hence, here we introduce Azahar, a computing environment for the creation, visualization and analysis of glycan molecules. Azahar is implemented in Python and works as a plugin for the well known PyMOL package (Schrodinger in The PyMOL molecular graphics system, version 1.3r1, 2010). Besides the already available visualization and analysis options provided by PyMOL, Azahar includes 3 cartoon-like representations and tools for 3D structure caracterization such as a comformational search using a Monte Carlo with minimization routine and also tools to analyse single glycans or trajectories/ensembles including the calculation of radius of gyration, Ramachandran plots and hydrogen bonds. Azahar is freely available to download from http://www.pymolwiki.org/index.php/Azahar and the source code is available at https://github.com/agustinaarroyuelo/Azahar.     

Peak alignment using wavelet pattern matching and differential evolution

Retention time shifts badly impair qualitative or quantitative results of chemometric analyses when entire chromatographic data are used. Hence, chromatograms should be aligned to perform further analysis. Being inspired and motivated by this purpose, a practical and handy peak alignment method (alignDE) is proposed, implemented in this research for one-way chromatograms, which basically consists of five steps: (1) chromatogram lengths equalization using linear interpolation; (2) accurate peak pattern matching by continuous wavelet transform (CWT) with the Mexican Hat and Haar wavelets as its mother wavelets; (3) flexible baseline fitting utilizing penalized least squares; (4) peak clustering when gap of two peaks is smaller than a certain threshold; (5) peak alignment using differential evolution (DE) to maximize linear correlation coefficient between reference signal and signal to be aligned. This method is demonstrated with both simulated chromatograms and real chromatograms, for example, chromatograms of fungal extracts and Red Peony Root obtained by HPLC-DAD. It is implemented in R language and available as open source software to a broad range of chromatograph users (http://code.google.com/p/alignde).     

Analysis of enantiomers giving partially overlapped peaks by using different treatments of the chromatographic ultraviolet signals: quantification of pseudoephedrine enantiomers

Different strategies for the quantification of partially coeluting optical isomers have been investigated. The methods tested are based on the use of different features as the analytical UV signals: peak heights, perpendicular drop areas, first and second derivatives of the chromatograms, peak areas obtained by deconvolution of the overlapped peaks with data fitting optimization, and a multivariate model (principal component regression, PCR). The amphetamine-derivative drug pseudoephedrine was selected as a model compound. For chromatography, LiChrospher 100 RP₁₈ and a mobile-phase consisting of methanol and a solution of carboxymethyl-β-cyclodextrin (the chiral selector) were used. The UV detector was set at 215 nm. The accuracy obtained with the tested methods at different degrees of overlapping and at different concentration ratios between enantiomers was evaluated. The results of this study demonstrated that the best option for quantification of partially overlapped UV peaks of enantiomers and to obtain the enatiomeric excess is the use of a PCR model using peak heights, perpendicular drop peak areas and deconvoluted peak areas as the original variables. The predictive ability of the proposed calibration model is of about 2–8 times better (depending on the overlapping degree) than that achieved with the other models tested.     

Linear Modulated Stochastic Resonance Algorithm Applied to Determination of Thidiazuron Residue in Water Using Stochastic Resonance

Abstract

The newly proposed linear modulated stochastic resonance algorithm (LSRA) was used to amplify and detect the weak chromatographic peaks of thidiazuron. The output chromatographic peak is often distorted when using the traditional stochastic resonance algorithm because of the existence of strong noise. In LSRA, the distortion of the output peak can be corrected by introducing a linear force into the nonlinear system. A two‐step optimization method was proposed to give attention to both the signal‐to‐noise ratio and the peak shape of output signal. The weak chromatographic peaks of thidiazuron can be amplified significantly and the distortion of the output peaks can be corrected using LSRA. The algorithm was used to detect thidiazuron residue in water with solid phase extraction‐high performance liquid chromatography. The limit of detection and limit of quantification were improved to 2.5 ng/l and 10 ng/l, respectively.