From the grapevine to the glass: A wine metabolomics tale by FT-ICR-MS.

Wine is one of the most consumed beverages around the world. Its unique characteristics arise from numerous processes, from the selection of grapevine varieties and grapes, the effect of the terroir and geographical origin, through the biochemical process of fermentation by microorganisms, until its aging. All molecules found in wine define its chemical fingerprint and can be used to tell the story of its origin, production, authenticity and quality. Wine's chemical composition can be characterized using an untargeted metabolomics approach based on extreme resolution mass spectrometry. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is currently the most powerful analytical technique to analyse such complex sample, providing the most comprehensive analysis of the chemical fingerprint of wine.

Photophysical image analysis: Unsupervised probabilistic thresholding for images from electron-multiplying charge-coupled devices.

We introduce the concept photophysical image analysis (PIA) and an associated pipeline for unsupervised probabilistic image thresholding for images recorded by electron-multiplying charge-coupled device (EMCCD) cameras. We base our approach on a closed-form analytic expression for the characteristic function (Fourier-transform of the probability mass function) for the image counts recorded in an EMCCD camera, which takes into account both stochasticity in the arrival of photons at the imaging camera and subsequent noise induced by the detection system of the camera. The only assumption in our method is that the background photon arrival to the imaging system is described by a stationary Poisson process (we make no assumption about the photon statistics for the signal). We estimate the background photon statistics parameter, λbg, from an image which contains both background and signal pixels by use of a novel truncated fit procedure with an automatically determined image count threshold. Prior to this, the camera noise model parameters are estimated using a calibration step. Utilizing the estimates for the camera parameters and λbg, we then introduce a probabilistic thresholding method, where, for the first time, the fraction of misclassified pixels can be determined a priori for a general image in an unsupervised way. We use synthetic images to validate our a priori estimates and to benchmark against the Otsu method, which is a popular unsupervised non-probabilistic image thresholding method (no a priori estimates for the error rates are provided). For completeness, we lastly present a simple heuristic general-purpose segmentation method based on the thresholding results, which we apply to segmentation of synthetic images and experimental images of fluorescent beads and lung cell nuclei. Our publicly available software opens up for fully automated, unsupervised, probabilistic photophysical image analysis.

Utilising Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to track the oxidation of lignin by an alkaliphilic laccase.

Lignin is a complex heteroaromatic polymer which is one of the most abundant and diverse biopolymers on the planet. It comprises approximately one third of all woody plant matter, making it an attractive candidate as an alternative, renewable feedstock to petrochemicals to produce fine chemicals. However, the inherent complexity of lignin makes it difficult to analyse and characterise using common analytical techniques, proving a hindrance to the utilisation of lignin as a green chemical feedstock. Herein we outline the tracking of lignin degradation by an alkaliphilic laccase in a semi-quantitative manner using a combined chemical analysis approach using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterise shifts in chemical diversity and relative abundance of ions, and NMR to highlight changes in the structure of lignin. Specifically, an alkaliphilic laccase was used to degrade an industrially relevant lignin, with compounds such as syringaresinol being almost wholly removed (95%) after 24 hours of treatment. Structural analyses reinforced these findings, indicating a >50% loss of NMR signal relating to ß-ß linkages, of which syringaresinol is representative. Ultimately, this work underlines a combined analytical approach that can be used to gain a broader semi-quantitative understanding of the enzymatic activity of laccases within a complex, non-model mixture.

Imaging Mass Spectrometry of Isotopically Resolved Intact Proteins on a Trapped Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometer.

In this work, we demonstrate rapid, high spatial, and high spectral resolution imaging of intact proteins by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on a hybrid quadrupole-reflectron time-of-flight (qTOF) mass spectrometer equipped with trapped ion mobility spectrometry (TIMS). Historically, untargeted MALDI IMS of proteins has been performed on TOF mass spectrometers. While advances in TOF instrumentation have enabled rapid, high spatial resolution IMS of intact proteins, TOF mass spectrometers generate relatively low-resolution mass spectra with limited mass accuracy. Conversely, the implementation of MALDI sources on high-resolving power Fourier transform (FT) mass spectrometers has allowed IMS experiments to be conducted with high spectral resolution with the caveat of increasingly long data acquisition times. As illustrated here, qTOF mass spectrometers enable protein imaging with the combined advantages of TOF and FT mass spectrometers. Protein isotope distributions were resolved for both a protein standard mixture and proteins detected from a whole-body mouse pup tissue section. Rapid (∼10 pixels/s) 10 µm lateral spatial resolution IMS was performed on a rat brain tissue section while maintaining isotopic spectral resolution. Lastly, proof-of-concept MALDI-TIMS data was acquired from a protein mixture to demonstrate the ability to differentiate charge states by ion mobility. These experiments highlight the advantages of qTOF and timsTOF platforms for resolving and interpreting complex protein spectra generated from tissue by IMS.

The processing of spatial frequencies through time in visual word recognition.

This study examined the temporal profile of spatial frequency processing in a word reading task in 16 normal adult readers. They had to report the word presented in a 200 ms display using a four-alternative forced-choice task (4AFC). The stimuli were made of an additive combination of the signal (i.e. the target word) and of a visual white noise patch wherein the signal-to-noise ratio varied randomly across stimulus duration. Four spatial frequency conditions were defined for the signal component of the stimulus (bandpass Butterworth filters with center frequencies of 1.2, 2.4, 4.8 and 9.6 cycles per degree). In contrast to the coarse-to-fine theory of visual recognition, the results show that the highest spatial frequency range dominates early processing, with a shift toward lower spatial frequencies at later points during stimulus exposure. This pattern interacted in a complex way with the temporal frequency content of signal-to-noise oscillations. The outcome of individual data patterns classification by a machine learning algorithm according to the corresponding spatial frequency band further shows that the most salient spatial frequency signature is obtained when the time dimension within data patterns is recoded into its Fourier transform.

Long-term, non-invasive FTIR detection of low-dose ionizing radiation exposure.

Non-invasive methods of detecting radiation exposure show promise to improve upon current approaches to biological dosimetry in ease, speed, and accuracy. Here we developed a pipeline that employs Fourier transform infrared (FTIR) spectroscopy in the mid-infrared spectrum to identify a signature of low dose ionizing radiation exposure in mouse ear pinnae over time. Mice exposed to 0.1 to 2 Gy total body irradiation were repeatedly measured by FTIR at the stratum corneum of the ear pinnae. We found significant discriminative power for all doses and time-points out to 90 days after exposure. Classification accuracy was maximized when testing 14 days after exposure (specificity > 0.9 with a sensitivity threshold of 0.9) and dropped by roughly 30% sensitivity at 90 days. Infrared frequencies point towards biological changes in DNA conformation, lipid oxidation and accumulation and shifts in protein secondary structure. Since only hundreds of samples were used to learn the highly discriminative signature, developing human-relevant diagnostic capabilities is likely feasible and this non-invasive procedure points toward rapid, non-invasive, and reagent-free biodosimetry applications at population scales.

Clustering honey samples with unsupervised machine learning methods using FTIR data.

This study utilizes Fourier transform infrared (FTIR) data from honey samples to cluster and categorize them based on their spectral characteristics. The aim is to group similar samples together, revealing patterns and aiding in classification. The process begins by determining the number of clusters using the elbow method, resulting in five distinct clusters. Principal Component Analysis (PCA) is then applied to reduce the dataset's dimensionality by capturing its significant variances. Hierarchical Cluster Analysis (HCA) further refines the sample clusters. 20% of the data, representing identified clusters, is randomly selected for testing, while the remainder serves as training data for a deep learning algorithm employing a multilayer perceptron (MLP). Following training, the test data are evaluated, revealing an impressive 96.15% accuracy. Accuracy measures the machine learning model's ability to predict class labels for new data accurately. This approach offers reliable honey sample clustering without necessitating extensive preprocessing. Moreover, its swiftness and cost-effectiveness enhance its practicality. Ultimately, by leveraging FTIR spectral data, this method successfully identifies similarities among honey samples, enabling efficient categorization and demonstrating promise in the field of spectral analysis in food science.

Fourier analysis of corneal irregular astigmatism after small-incision lenticule extraction and transepithelial photorefractive keratectomy: A comparative study.

To compare changes in the spherical component, regular astigmatism, and irregular astigmatism of the anterior surface of the cornea after small-incision lenticule extraction (SMILE) and transepithelial photorefractive keratectomy (TransPRK). Fifty-six patients underwent SMILE in 56 eyes, and 68 patients underwet TransPRK in 68 eyes. The right eye was chosen to enter the group. Six months after the procedure, Scheimpflug images were acquired, and Fourier analysis of the anterior surface of patients' corneas was performed using the Pentacam built-in software. Fourier parameters encompass various measurements such as the steepest radius of the curvature and average eccentricity of the spherical components (SphRmin and SphEcc), maximum decentration (MaxDec), central and peripheral regular astigmatism (regular astigmatism at the center [AstC] and regular astigmatism at the periphery [AstP]), and irregularity (Irr). At 6 months postoperatively, SphEcc decreased significantly (P < .001), MaxDec increased significantly (P < .001), and Irr increased insignificantly (P = .254) in the SMILE group. SphEcc decreased significantly (P < .001) and MaxDec and Irr increased significantly (P < .001) in the TransPRK group. TransPRK caused greater changes in SphEcc, MaxDec, and Irr on the anterior corneal surface than SMILE (P < .05). The amount of MaxDec-induced changes in SMILE and TransPRK was significantly correlated with the amount of higher-order aberrations and spherical aberration changes (P < .05). SMILE and TransPRK increase overall irregular astigmatism on the anterior surface of the cornea, more so with TransPRK, where changes in decentration are associated with with increased higher-order aberrations.

Quantitative or qualitative biomolecular changes in blood serum composition induced by childhood obesity: A Fourier transform infrared examination.

Childhood obesity (CO) negatively affects one in three children and stands as the fourth most common risk factor of health and well-being. Clarifying the molecular and structural modifications that transpire during the development of obesity is crucial for understanding its progression and devising effective therapies. The study was indeed conducted as part of an ongoing CO treatment trial, where data were collected from children diagnosed with CO before the initiation of non-drug treatment interventions. Our primary aim was to analyze the biochemical changes associated with childhood obesity, specifically focusing on concentrations of lipids, lipoproteins, insulin, and glucose. By comparing these parameters between the CO group (n = 60) and a control group of healthy children (n = 43), we sought to elucidate the metabolic differences present in individuals with CO. Our biochemical analyses unveiled lower LDL (low-density lipoproteins) levels and higher HDL (high-density lipoproteins), cholesterol, triglycerides, insulin, and glucose levels in CO individuals compared to controls. To scrutinize these changes in more detail, we employed Fourier transform infrared (FTIR) spectroscopy on the serum samples. Our results indicated elevated levels of lipids and proteins in the serum of CO, compared to controls. Additionally, we noted structural changes in the vibrations of glucose, ß-sheet, and lipids in CO group. The FTIR technique, coupled with principal component analysis (PCA), demonstrated a marked differentiation between CO and controls, particularly in the FTIR region corresponding to amide and lipids. The Pearson test revealed a stronger correlation between biochemical data and FTIR spectra than between 2nd derivative FTIR spectra. Overall, our study provides valuable insights into the molecular and structural changes occurring in CO.

Classification of asbestos and their nonasbestiform analogues using FTIR and multivariate data analysis.

This study presents a possible application of Fourier transform infrared (FTIR) spectrometry and multivariate data analysis, principal component analysis (PCA), and partial least squares-discriminant analysis (PLS-DA) for classifying asbestos and their nonasbestiform analogues. The objectives of the study are: 1) to classify six regulated asbestos types and 2) to classify between asbestos types and their nonasbestiform analogues. The respirable fraction of six regulated asbestos types and their nonasbestiform analogues were prepared in potassium bromide pellets and collected on polyvinyl chloride membrane filters for FTIR measurement. Both PCA and PLS-DA classified asbestos types and their nonasbestiform analogues on the score plots showed a very distinct clustering of samples between the serpentine (chrysotile) and amphibole groups. The PLS-DA model provided ∼95% correct prediction with a single asbestos type in the sample, although it did not provide all correct predictions for all the challenge samples due to their inherent complexity and the limited sample number. Further studies are necessary for a better prediction level in real samples and standardization of sampling and analysis procedures.

FTIR microspectroscopic study of gastric cancer AGS cells apoptosis induced by As2O3.

As2O3 has shown significant anti-gastric cancer effects, but the mechanism is still unclear. Thus, biomacromolecular changes induced by As2O3 were investigated by using human gastric cancer AGS cells as the model. Flow cytometry results confirmed that As2O3 induced AGS cells apoptosis. Fourier transform infrared (FTIR) microspectroscopy detected biomacromolecular changes during As2O3-induced AGS cells apoptosis sensitively: IR spectra showed significant changes in the lipids content and the proteins and DNA structure. Peak-area ratios indicated obvious changes in the lipids and DNA content and the proteins structure, while also showing a relatively good linear relationship between A1733/A969 and the apoptosis rate. PCA exhibited significant alteration in nucleic acids while curve fitting further revealed the changes in nucleic acids and proteins. On the whole, our study explored As2O3-induced gastric cancer cells apoptosis in depth on the basis of analyzing biomacromolecular changes, in addition, it also suggested FTIR microspectroscopy to be possibly useful in the research of apoptosis.

A rapid method for identification of Lanxangia tsaoko origin and fruit shape: FT-NIR combined with chemometrics and image recognition.

Lanxangia tsaoko's accurate classifications of different origins and fruit shapes are significant for research in L. tsaoko difference between origin and species as well as for variety breeding, cultivation, and market management. In this work, Fourier transform-near infrared (FT-NIR) spectroscopy was transformed into two-dimensional and three-dimensional correlation spectroscopies to further investigate the spectral characteristics of L. tsaoko. Before building the classification model, the raw FT-NIR spectra were preprocessed using multiplicative scatter correction and second derivative, whereas principal component analysis, successive projections algorithm, and competitive adaptive reweighted sampling were used for spectral feature variable extraction. Then combined with partial least squares-discriminant analysis (PLS-DA), support vector machine (SVM), decision tree, and residual network (ResNet) models for origin and fruit shape discriminated in L. tsaoko. The PLS-DA and SVM models can achieve 100% classification in origin classification, but what is difficult to avoid is the complex process of model optimization. The ResNet image recognition model classifies the origin and shape of L. tsaoko with 100% accuracy, and without the need for complex preprocessing and feature extraction, the model facilitates the realization of fast, accurate, and efficient identification.

Fourier Ptychographic Microscopy 10 Years on: A Review.

Fourier ptychographic microscopy (FPM) emerged as a prominent imaging technique in 2013, attracting significant interest due to its remarkable features such as precise phase retrieval, expansive field of view (FOV), and superior resolution. Over the past decade, FPM has become an essential tool in microscopy, with applications in metrology, scientific research, biomedicine, and inspection. This achievement arises from its ability to effectively address the persistent challenge of achieving a trade-off between FOV and resolution in imaging systems. It has a wide range of applications, including label-free imaging, drug screening, and digital pathology. In this comprehensive review, we present a concise overview of the fundamental principles of FPM and compare it with similar imaging techniques. In addition, we present a study on achieving colorization of restored photographs and enhancing the speed of FPM. Subsequently, we showcase several FPM applications utilizing the previously described technologies, with a specific focus on digital pathology, drug screening, and three-dimensional imaging. We thoroughly examine the benefits and challenges associated with integrating deep learning and FPM. To summarize, we express our own viewpoints on the technological progress of FPM and explore prospective avenues for its future developments.

Domain transformation learning for MR image reconstruction from dual domain input.

Medical images are acquired through diverse imaging systems, with each system employing specific image reconstruction techniques to transform sensor data into images. In MRI, sensor data (i.e., k-space data) is encoded in the frequency domain, and fully sampled k-space data is transformed into an image using the inverse Fourier Transform. However, in efforts to reduce acquisition time, k-space is often subsampled, necessitating a sophisticated image reconstruction method beyond a simple transform. The proposed approach addresses this challenge by training a model to learn domain transform, generating the final image directly from undersampled k-space input. Significantly, to improve the stability of reconstruction from randomly subsampled k-space data, folded images are incorporated as supplementary inputs in the dual-input ETER-net. Moreover, modifications are made to the formation of inputs for the bi-RNN stages to accommodate non-fixed k-space trajectories. Experimental validation, encompassing both regular and irregular sampling trajectories, validates the method's effectiveness. The results demonstrated superior performance, measured by PSNR, SSIM, and VIF, across acceleration factors of 4 and 8. In summary, the dual-input ETER-net emerges as an effective both regular and irregular sampling trajectories, and accommodating diverse acceleration factors.

Validating computer applications for calculating spatial resolution and noise property in CT using simulated images with known properties.

The purpose of this study was to evaluate, using simulated images with known property values, how accurately some computer applications for calculating modulation transfer function (MTF), task transfer function (TTF), or noise power spectrum (NPS) in computed tomography (CT) based on widely known techniques produce their results. Specifically, they were three applications applicable to the wire method for MTF calculation, two applications corresponding to the circular edge (CE) and linear edge (LE) methods for TTF, and one application using a two-dimensional Fourier transform for NPS, which are collectively integrated with the software 'CTmeasure' provided by the Japanese Society of CT Technology. Images for the calculation with radial symmetry were generated based on a roll-off type filter function. The accuracy of each application was evaluated by comparing the calculated property with the true one. The calculated MTFs for the wire method accurately matched the true ones with percentage errors of smaller than 1.0%. In contrast, the CE and LE methods presented relatively large errors of up to 50% at high frequencies, whereas the NPS's errors were up to 30%. A closer investigation revealed, however, that these errors were attributable not to the applications but to the insufficiencies in the measurement techniques commonly employed. By improving the measurement conditions to minimize the effects of the insufficiencies, the errors notably decreased, whichvalidated the calculation techniques in the applications we used.

A review of concepts and methods for FTIR imaging of biomarker changes in the post-stroke brain.

Stroke represents a core area of study in neurosciences and public health due to its global contribution toward mortality and disability. The intricate pathophysiology of stroke, including ischemic and hemorrhagic events, involves the interruption in oxygen and nutrient delivery to the brain. Disruption of these crucial processes in the central nervous system leads to metabolic dysregulation and cell death. Fourier transform infrared (FTIR) spectroscopy can simultaneously measure total protein and lipid content along with a number of key biomarkers within brain tissue that cannot be observed using conventional techniques. FTIR imaging provides the opportunity to visualize this information in tissue which has not been chemically treated prior to analysis, thus retaining the spatial distribution and in situ chemical information. Here we present a review of FTIR imaging methods for investigating the biomarker responses in the post-stroke brain.

User identification system based on 2D CQT spectrogram of EMG with adaptive frequency resolution adjustment.

User identification systems based on electromyogram (EMG) signals, generated inside the body in different signal patterns and exhibiting individual characteristics based on muscle development and activity, are being actively researched. However, nonlinear and abnormal signals constrain conventional user identification using EMG signals in improving accuracy by using the 1-D feature from each time and frequency domain. Therefore, multidimensional features containing time-frequency information extracted from EMG signals have attracted much attention to improving identification accuracy. We propose a user identification system using constant Q transform (CQT) based 2D features whose time-frequency resolution is customized according to EMG signals. The proposed user identification system comprises data preprocessing, CQT-based 2D image conversion, convolutional feature extraction, and classification by convolutional neural network (CNN). The experimental results showed that the accuracy of the proposed user identification system using CQT-based 2D spectrograms was 97.5%, an improvement of 15.4% and 2.1% compared to the accuracy of 1D features and short-time Fourier transform (STFT) based user identification, respectively.

In situ Fourier transform infrared-attenuated total reflection spectroscopy and modeling investigation of protein adsorption: Case of expanded bovine serum albumin on titanium dioxide anatase.

The purpose of this experimental and modeling research is to study the pH effect and to determine the surface coverage plus the adsorption constant (Ka) of bovine serum albumin (BSA) protein adsorbed on TiO2 anatase surface, respectively. In situ Fourier transform infrared-attenuated total reflection spectroscopy in a flow-through cell was used to study the BSA adsorption on porous TiO2 anatase films. The experiments were performed in water solution, under different pH values, at a concentration of 10-6 mol/l. Theoretically, we extended the two-state model, based on a system of coupled differential equations, by adding a desorption parameter Kd2, for unfolded state. The model was solved taking into account the adsorption (Ka), desorption (Kd1,2), transformation (Kf) coefficients, and the initial solution protein concentration (C0). The findings clearly illustrated that the solution pH drastically changed the behavior of BSA adsorption, whereas the mathematical analytical solutions allowed us to determine the native state (θ1), the unfolded state (θ2), and the full one (θ) surface coverages. Finally, a good application of the approximated model on the experimental work, expanded BSA adsorbed on TiO2 anatase at pH = 1.7, indicated a value of Ka = (408.36 ± 0.996) × 102 mol-1 l min-1.

Fast screening using attenuated total reflectance- fourier transform infrared (ATR-FTIR) spectroscopy of patients based on D-dimer threshold value.

Attenuated Total Reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is an emerging technology in the medical field. Blood D-dimer was initially studied as a marker of the activation of coagulation and fibrinolysis. It is mainly used as a potential diagnosis screening test for pulmonary embolism or deep vein thrombosis but was recently associated with COVID-19 severity. This study aimed to evaluate the use of ATR-FTIR spectroscopy with machine learning to classify plasma D-dimer concentrations. The plasma ATR-FTIR spectra from 100 patients were studied through principal component analysis (PCA) and two supervised approaches: genetic algorithm with linear discriminant analysis (GA-LDA) and partial least squares with linear discriminant (PLS-DA). The spectra were truncated to the fingerprint region (1800-1000 cm-1). The GA-LDA method effectively classified patients according to D-dimer cutoff (≤0.5 µg/mL and >0.5 µg/mL) with 87.5 % specificity and 100 % sensitivity on the training set, and 85.7 % specificity, and 95.6 % sensitivity on the test set. Thus, we demonstrate that ATR-FTIR spectroscopy might be an important additional tool for classifying patients according to D-dimer values. ATR-FTIR spectral analyses associated with clinical evidence can contribute to a faster and more accurate medical diagnosis, reduce patient morbidity, and save resources and demand for professionals.

Two-trace two-dimensional correlation spectra (2T2D-COS) analysis using FTIR spectra to monitor the immune response by COVID-19.

There is a growing trend in using saliva for SARS-CoV-2 detection with reasonable accuracy. We have studied the responses of IgA, IgG, and IgM in human saliva by directly comparing disease with control analyzing two-trace two-dimensional correlation spectra (2T2D-COS) employing Fourier transform infrared (FTIR) spectra. It explores the molecular-level variation between control and COVID-19 saliva samples. The advantage of 2T2D spectra is that it helps in discriminating remarkably subtle features between two simple pairs of spectra. It gives spectral information from highly overlapped bands associated with different systems. The clinical findings from 2T2D show the decrease of IgG and IgM salivary antibodies in the 50, 60, 65, and 75-years COVID-19 samples. Among the various COVID-19 populations studied the female 30-years group reveals defense mechanisms exhibited by IgM and IgA. Lipids and fatty acids decrease, resulting in lipid oxidation due to the SARS-CoV-2 in the samples studied. Study shows salivary thiocyanate plays defense against SARS-CoV-2 in the male population in 25 and 35 age groups. The receiver operation characteristics statistical method shows a sensitivity of 98% and a specificity of 94% for the samples studied. The measure of accuracy computed as F score and G score has a high value, supporting our study's validation. Thus, 2T2D-COS analysis can potentially monitor the progression of immunoglobulin's response function to COVID-19 with reasonable accuracy, which could help diagnose clinical trials. KEY MESSAGES: The molecular profile of salivary antibodies is well resolved and identified from 2T2D-COS FTIR spectra. The IgG antibody plays a significant role in the defense mechanism against SARS-CoV-2 in 25-40 years. 2T2D-COS reveals the absence of salivary thiocyanate in the 40-75 years COVID-19 population. The receiver operation characteristic (ROC) analysis validates our study with high sensitivity and specificity.