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Science Progress Sep 2017Since the original observation by Zeeman, that spectral lines can be affected by magnetic fields, 'magnetic spectroscopy' has evolved into the broad arsenal of... (Review)
Review
Since the original observation by Zeeman, that spectral lines can be affected by magnetic fields, 'magnetic spectroscopy' has evolved into the broad arsenal of techniques known as 'magnetic resonance'. This review focuses on nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), and muon spin resonance (μSR): methods which have provided unparalleled insight into the structures, reactivity and dynamics of molecules, and thereby contributed to a detailed understanding of important aspects of chemistry, and the materials, biomedical, and environmental sciences. Magnetic resonance imaging (MRI), in vivo magnetic resonance spectroscopy (MRS) and functional magnetic resonance spectroscopy (fMRS) are also described. EPR is outlined as a principal method for investigating free radicals, along with biomedical applications, and mention is given to the more recent innovation of pulsed EPR techniques. In the final section of the article, the various methods known as μSR are collected under the heading 'muon spin resonance', in order to emphasise their complementarity with the more familiar NMR and EPR.
Topics: Electron Spin Resonance Spectroscopy; Fourier Analysis; Free Radicals; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy
PubMed: 28779760
DOI: 10.3184/003685017X14993478654307 -
Journal of Magnetic Resonance (San... Oct 2017Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford...
Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development.
Topics: Algorithms; Computers; Data Interpretation, Statistical; Fourier Analysis; Magnetic Resonance Spectroscopy; Signal Processing, Computer-Assisted; Software
PubMed: 28385517
DOI: 10.1016/j.jmr.2017.03.017 -
BMC Bioinformatics Aug 2022Amino acid property-aware phylogenetic analysis (APPA) refers to the phylogenetic analysis method based on amino acid property encoding, which is used for understanding...
BACKGROUND
Amino acid property-aware phylogenetic analysis (APPA) refers to the phylogenetic analysis method based on amino acid property encoding, which is used for understanding and inferring evolutionary relationships between species from the molecular perspective. Fast Fourier transform (FFT) and Higuchi's fractal dimension (HFD) have excellent performance in describing sequences' structural and complexity information for APPA. However, with the exponential growth of protein sequence data, it is very important to develop a reliable APPA method for protein sequence analysis.
RESULTS
Consequently, we propose a new method named FFP, it joints FFT and HFD. Firstly, FFP is used to encode protein sequences on the basis of the important physicochemical properties of amino acids, the dissociation constant, which determines acidity and basicity of protein molecules. Secondly, FFT and HFD are used to generate the feature vectors of encoded sequences, whereafter, the distance matrix is calculated from the cosine function, which describes the degree of similarity between species. The smaller the distance between them, the more similar they are. Finally, the phylogenetic tree is constructed. When FFP is tested for phylogenetic analysis on four groups of protein sequences, the results are obviously better than other comparisons, with the highest accuracy up to more than 97%.
CONCLUSION
FFP has higher accuracy in APPA and multi-sequence alignment. It also can measure the protein sequence similarity effectively. And it is hoped to play a role in APPA's related research.
Topics: Algorithms; Amino Acids; Fourier Analysis; Fractals; Phylogeny; Proteins
PubMed: 35986255
DOI: 10.1186/s12859-022-04889-3 -
Mass Spectrometry Reviews Mar 2022Research in the field of neurobiology and neurochemistry has seen a rapid expansion in the last several years due to advances in technologies and instrumentation,... (Review)
Review
Research in the field of neurobiology and neurochemistry has seen a rapid expansion in the last several years due to advances in technologies and instrumentation, facilitating the detection of biomolecules critical to the complex signaling of neurons. Part of this growth has been due to the development and implementation of high-resolution Fourier transform (FT) mass spectrometry (MS), as is offered by FT ion cyclotron resonance (FTICR) and Orbitrap mass analyzers, which improves the accuracy of measurements and helps resolve the complex biological mixtures often analyzed in the nervous system. The coupling of matrix-assisted laser desorption/ionization (MALDI) with high-resolution MS has drastically expanded the information that can be obtained with these complex samples. This review discusses notable technical developments in MALDI-FTICR and MALDI-Orbitrap platforms and their applications toward molecules in the nervous system, including sequence elucidation and profiling with de novo sequencing, analysis of post-translational modifications, in situ analysis, key advances in sample preparation and handling, quantitation, and imaging. Notable novel applications are also discussed to highlight key developments critical to advancing our understanding of neurobiology and providing insight into the exciting future of this field. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
Topics: Cyclotrons; Fourier Analysis; Neurobiology; Specimen Handling; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 33165982
DOI: 10.1002/mas.21661 -
Applied Spectroscopy Jan 2022Infrared (IR) spectroscopic imaging instruments' performance can be characterized and optimized by an analysis of their limit of detection (LOD). Here we report a...
Infrared (IR) spectroscopic imaging instruments' performance can be characterized and optimized by an analysis of their limit of detection (LOD). Here we report a systematic analysis of the LOD for Fourier transform IR (FT-IR) and discrete frequency IR (DFIR) imaging spectrometers. In addition to traditional measurements of sample and blank data, we propose a decision theory perspective to pose the determination of LOD as a binary classification problem under different assumptions of noise uniformity and correlation. We also examine three spectral analysis approaches, namely, absorbance at a single frequency, average of absorbance over selected frequencies and total spectral distance - to suit instruments that acquire discrete or contiguous spectral bandwidths. The analysis is validated by refining the fabrication of a bovine serum albumin protein microarray to provide eight uniform spots from ∼2.8 nL of solution for each concentration over a wide range (0.05-10 mg/mL). Using scanning parameters that are typical for each instrument, we estimate a LOD of 0.16 mg/mL and 0.12 mg/mL for widefield and line scanning FT-IR imaging systems, respectively, using the spectral distance approach, and 0.22 mg/mL and 0.15 mg/mL using an optimal set of discrete frequencies. As expected, averaging and the use of post-processing techniques such as minimum noise fraction transformation results in LODs as low as ∼0.075 mg/mL that correspond to a spotted protein mass of ∼112 fg/pixel. We emphasize that these measurements were conducted at typical imaging parameters for each instrument and can be improved using the usual trading rules of IR spectroscopy. This systematic analysis and methodology for determining the LOD can allow for quantitative measures of confidence in imaging an analyte's concentration and a basis for further improving IR imaging technology.
Topics: Fourier Analysis; Limit of Detection; Proteins; Spectrophotometry, Infrared; Spectroscopy, Fourier Transform Infrared
PubMed: 34643135
DOI: 10.1177/00037028211050961 -
Mass Spectrometry Reviews Mar 2022The set of all intra- and intermolecular interactions, collectively known as the interactome, is currently an unmet challenge for any analytical method, but if measured,... (Review)
Review
The set of all intra- and intermolecular interactions, collectively known as the interactome, is currently an unmet challenge for any analytical method, but if measured, could provide unparalleled insight on molecular function in living systems. Developments and applications of chemical cross-linking and high-performance mass spectrometry technologies are beginning to reveal details on how proteins interact in cells and how protein conformations and interactions inside cells change with phenotype or during drug treatment or other perturbations. A major contributor to these advances is Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) technology and its implementation with accurate mass measurements on cross-linked peptide-pair precursor and fragment ions to enable improved identification methods. However, these applications place increased demands on mass spectrometer performance in terms of high-resolution spectral acquisition rates for on-line MS experiments. Moreover, FT-ICR-MS also offers unique opportunities to develop and implement parallel ICR cells for multiplexed signal acquisition and the potential to greatly advance accurate mass acquisition rates for interactome studies. This review highlights our efforts to exploit accurate mass FT-ICR-MS technologies with chemical cross-linking and developments being pursued to realize parallel MS array capabilities that will further advance visualization of the interactome.
Topics: Cyclotrons; Fourier Analysis; Ions; Mass Spectrometry; Proteins
PubMed: 33289940
DOI: 10.1002/mas.21675 -
Neuron Apr 2019Filters are commonly used to reduce noise and improve data quality. Filter theory is part of a scientist's training, yet the impact of filters on interpreting data is... (Review)
Review
Filters are commonly used to reduce noise and improve data quality. Filter theory is part of a scientist's training, yet the impact of filters on interpreting data is not always fully appreciated. This paper reviews the issue and explains what a filter is, what problems are to be expected when using them, how to choose the right filter, and how to avoid filtering by using alternative tools. Time-frequency analysis shares some of the same problems that filters have, particularly in the case of wavelet transforms. We recommend reporting filter characteristics with sufficient details, including a plot of the impulse or step response as an inset.
Topics: Artifacts; Causality; Data Accuracy; Fourier Analysis; Humans; Neurosciences; Signal Processing, Computer-Assisted; Signal-To-Noise Ratio; Wavelet Analysis
PubMed: 30998899
DOI: 10.1016/j.neuron.2019.02.039 -
Progress in Nuclear Magnetic Resonance... Nov 2014Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID)... (Review)
Review
Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR.
Topics: Fourier Analysis; Humans; Magnetic Resonance Spectroscopy; Signal Processing, Computer-Assisted
PubMed: 25456315
DOI: 10.1016/j.pnmrs.2014.09.002 -
Scientific Reports Oct 2023Dengue hemorrhagic fever is a worldwide epidemic caused by dengue virus and spread by infected female mosquitoes. The two main mosquito species vectors of the dengue...
Dengue hemorrhagic fever is a worldwide epidemic caused by dengue virus and spread by infected female mosquitoes. The two main mosquito species vectors of the dengue virus are Aedes aegypti and Aedes albopictus. Conventionally, the identification of these two species' egg is time-consuming which makes vector control more difficult. However, although attempts on efficiency improvements by providing automatic identification have been conducted, the earliest stage is at the larval stage. In addition, there are currently no studies on classifying to distinguish the two vectors during the egg stage based on their digital image. A total of 140 egg images of Aedes aegypti and Aedes albopictus were collected and validated by rearing them individually to become adult mosquitoes. Image processing and elliptic Fourier analysis were carried out to extract and describe the shape difference of the two vectors' eggs. Machine learning algorithms were then used to classify the shape signatures. Morphometrically, the two species' eggs were significantly different, which Aedes albopictus were smaller in size. Egg-shape contour reconstructions of principal components and Multivariate Analysis of Variance (MANOVA) revealed that there is a significant difference (p value [Formula: see text]) in shape between two species' eggs at the posterior end. Based on Wilk's lambda of the MANOVA results, the classification could be done using only the first 3 principal components. Classification of the test data yielded an accuracy of 85.00% and F1 score 84.21% with Linear Discriminant Analysis applying default hyperparameter. Alternatively, k-Nearest Neighbors with optimal hyperparameter yielded a higher classification result with 87.50% and 87.18% of accuracy and F1 score, respectively. These results demonstrate that the proposed method can be used to classify Aedes aegypti and Aedes albopictus eggs based on their digital image. This method provides a foundation for improving the identification and surveillance of the two vectors and decision making in developing vector control strategies.
Topics: Animals; Female; Dengue; Dengue Virus; Aedes; Insect Vectors; Fourier Analysis
PubMed: 37833335
DOI: 10.1038/s41598-023-28510-6 -
Sensors (Basel, Switzerland) Apr 2022The sweep rate of conventional short-cavity lasers with an intracavity-swept filter is limited by the buildup time of laser signals from spontaneous emissions. The... (Review)
Review
The sweep rate of conventional short-cavity lasers with an intracavity-swept filter is limited by the buildup time of laser signals from spontaneous emissions. The Fourier domain mode-locked (FDML) laser was proposed to overcome the limitations of buildup time by inserting a long fiber delay in the cavity to store the whole swept signal and has attracted much interest in both theoretical and experimental studies. In this review, the theoretical models to understand the dynamics of the FDML laser and the experimental techniques to realize high speed, wide sweep range, long coherence length, high output power and highly stable swept signals in FDML lasers will be discussed. We will then discuss the applications of FDML lasers in optical coherence tomography (OCT), fiber sensing, precision measurement, microwave generation and nonlinear microscopy.
Topics: Equipment Design; Fourier Analysis; Lasers; Light; Tomography, Optical Coherence
PubMed: 35590839
DOI: 10.3390/s22093145