Enhancing Compression Level for More Efficient Compressed Sensing and Other Lessons from NMR Spectroscopy

Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes

The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few "significant" points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to "conventional" compressed sensing. We exemplify the concept of "difference CS" with one such case-the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.

Compressed Sensing Technique for the Localization of Harmonic Distortions in Electrical Power Systems

The present work proposes to locate harmonic frequencies that distort the fundamental voltage and current waves in electrical systems using the compressed sensing (CS) technique. With the compressed sensing algorithm, data compression is revolutionized, a few samples are taken randomly, a measurement matrix is formed, and according to a linear transformation, the signal is taken from the time domain to the frequency domain in a compressed form. Then, the inverse linear transformation is used to reconstruct the signal with a few sensed samples of an electrical signal. Therefore, to demonstrate the benefits of CS in the detection of harmonics in the electrical network of this work, power quality analyzer equipment (commercial) is used. It measures the current of a nonlinear load and issues its results of harmonic current distortion (THD-I) on its screen and the number of harmonics detected in the network; this equipment acquires the data based on the Shannon-Nyquist theorem taken as a standard of measurement. At the same time, an electronic prototype senses the current signal of the nonlinear load. The prototype takes data from the current signal of the nonlinear load randomly and incoherently, so it takes fewer samples than the power quality analyzer equipment used as a measurement standard. The data taken by the prototype are entered into the Matlab software via USB, and the CS algorithm run and delivers, as a result, the harmonic distortions of the current signal THD-I and the number of harmonics. The results obtained with the compressed sensing algorithm versus the standard measurement equipment are analyzed, the error is calculated, and the number of samples taken by the standard equipment and the prototype, the machine time, and the maximum sampling frequency are analyzed.

Newton meets Ockham: Parameter estimation and model selection of NMR data with NMR-EsPy

We present NMR-EsPy (NMR Estimation in Python), a versatile, simple-to-use Python package for estimating the signal parameters that describe one-dimensional time-domain NMR data. The software is fully integrated into Topspin, a widely used NMR platform, and comes with a Graphical User Interface, allowing users unfamiliar with the underlying theory and/or Python programming to access the full functionality of the software package. NMR-EsPy utilises Newton's method, an iterative non-linear programming technique. By including the variance of oscillator phases in the optimization, NMR-EsPy can generate parsimonious parameter estimates, giving NMR users access to meaningful quantitative information. This principle is easily extendable to study specific regions of an NMR spectrum to reduce computational cost. The complete mathematical treatment along with examples of the implementation of the estimation routine are presented.

Benefits of time-resolved nonuniform sampling in reaction monitoring: The case of aza-Michael addition of benzylamine and acrylamide

Monitoring of chemical reactions is best carried out using methods that sample the test object at a rate greater than the time scale of the processes taking place. The recently proposed time-resolved nonuniform sampling (TR-NUS) method allows the use of two-dimensional (2D) nuclear magnetic resonance (NMR) spectra for this purpose and provides a time resolution equivalent to that achievable using one-dimensional spectra. Herein, we show that TR-NUS acquired data eliminates 2D spectral line disturbances and enables more accurate signal integration and kinetics conclusions. The considerations are exemplified with a seemingly simple aza-Michael reaction of benzylamine and acrylamide. Surprisingly, the product identification is possible only using 2D spectra, although credible monitoring requires TR-NUS.

Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy

NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time-consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated under several different conditions, for example, to measure the temperature-dependent effects in a spectrum (temperature coefficients (TCs)). Herein, a new approach that involves joint sampling of indirect evolution times and temperature is proposed. This allows TCs to be measured through 3D spectra in even less time than that needed to acquire a single spectrum by using the conventional approach. Two signal processing methods that are complementary, in terms of sensitivity and resolution, 1) dividing data into overlapping subsets followed by compressed sensing reconstruction, and 2) treating the complete data set with a variant of the Radon transform, are proposed. The temperature-swept 3D HNCO spectra of two intrinsically disordered proteins, osteopontin and CD44 cytoplasmic tail, show that this new approach makes it possible to determine TCs and their non-linearities effectively. Non-linearities, which indicate the presence of a compact state, are particularly interesting. The complete package of data acquisition and processing software for this new approach are provided.

Signal-Processing Framework for Ultrasound Compressed Sensing Data: Envelope Detection and Spectral Analysis

Acquisition times and storage requirements have become increasingly important in signal-processing applications, as the sizes of datasets have increased. Hence, compressed sensing (CS) has emerged as an alternative processing technique, as original signals can be reconstructed using fewer data samples collected at frequencies below the Nyquist sampling rate. However, further analysis of CS data in both time and frequency domains requires the reconstruction of the original form of the time-domain data, as traditional signal-processing techniques are designed for uncompressed data. In this paper, we propose a signal-processing framework that extracts spectral properties for frequency-domain analysis directly from under-sampled ultrasound CS data, using an appropriate basis matrix, and efficiently converts this into the envelope of a time-domain signal, avoiding full reconstruction. The technique generates more accurate results than the traditional framework in both time- and frequency-domain analyses, and is simpler and faster in execution than full reconstruction, without any loss of information. Hence, the proposed framework offers a new standard for signal processing using ultrasound CS data, especially for small and portable systems handling large datasets.