{"title":"Enhancing Generalization and Mitigating Overfitting in Deep Learning for Brain Cancer Diagnosis from MRI","authors":"Mohamad Abou Ali, Jinan Charafeddine, Fadi Dornaika, Ignacio Arganda-Carreras","doi":"10.1007/s00723-024-01743-y","DOIUrl":"10.1007/s00723-024-01743-y","url":null,"abstract":"<div><p>Brain cancer represents a significant global health challenge with increasing incidence and mortality rates. Magnetic Resonance Imaging (MRI) plays a pivotal role in early detection and treatment planning. This study adopts a systematic approach across four phases: (1) Optimal Model Selection using the Adam optimizer, emphasizing accuracy metrics, weight computation, early stopping, and ReduceLROnPlateau techniques. (2) Real-world Scenario Simulation through synthetic perturbed datasets created by applying noise, blur (to simulate various magnetic field strengths: 1T, 1.5T, 3T), and patient motion artifacts (mimicking MRI scanning motion effects) to the testing data from the BT-MRI dataset, an online published brain tumor MRI dataset. (3) Optimization involving a range of optimizers (Adam, Adagrad, Nadam, RMSprop, SGD) and online augmentation techniques (AutoMix, CutMix, LGCOAMix, PatchUp). (4) Solution Exploration integrating Gaussian Noise and Blur as augmentation strategies during training to enhance model generalization under diverse conditions. Initial evaluations achieved strong performance, consistently reaching 99.45% accuracy on the BT-MRI dataset. However, testing against synthetic perturbed datasets mimicking real-world conditions revealed challenges in maintaining robust model performance. Despite employing diverse optimization methods and advanced augmentation techniques, this study identifies persistent challenges in ensuring model robustness with synthetic perturbed datasets. Notably, the integration of Gaussian Noise and Blur during training significantly improved model resilience. This research underscores the critical role of methodological rigor and innovative augmentation strategies in advancing deep learning applications for precise brain cancer diagnosis using MRI.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 3","pages":"359 - 394"},"PeriodicalIF":1.1,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Derivation of Multi-Exponential Magnetic Resonance Relaxation Equations in Simple Pore Geometries","authors":"Armin Afrough","doi":"10.1007/s00723-024-01729-w","DOIUrl":"10.1007/s00723-024-01729-w","url":null,"abstract":"<div><p>The common interpretation of magnetic resonance relaxation time distribution of liquids in porous media assumes a one-to-one relationship between the pore size and the relaxation time constants. This common conviction may not be correct in many microporous materials. Each pore size may be associated with more than one peak in the NMR relaxation time distributions: a single dominant peak and also possibly one or a few minor peaks. The appearance of minor peaks is due to the non-vanishing nonground eigenvalues of the diffusion–relaxation equation. Brownstein and Tarr (Phys Rev A 19:2446, 1979) described these features, but their solutions at conditions beyond the fast-diffusion regime are not widely adopted. We provide the derivation of Brownstein–Tarr equations for multi-exponential magnetic resonance relaxation decay for liquids in simple pore geometries. General solutions are presented for planar, cylindrical, and spherical pores—as well as two limiting cases of fast and slow diffusion for each geometry. Similar solutions are also relevant to first-order dilute reactions in porous media in heterogeneous reaction–diffusion systems. We hope that the availability of these derivations helps wider adoption of more realistic interpretation of magnetic resonance relaxation in porous media in the light of the multi-exponential Brownstein–Tarr model.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 3","pages":"313 - 358"},"PeriodicalIF":1.1,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00723-024-01729-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Svetlana V. Kurmaz, Ksenia V. Panicheva, Irina A. Avilova, Sergey G. Vasil’ev
{"title":"Preparation of Water-Soluble Tocopherol Compositions Based on N-Vinylpyrrolidone Polymers and Exploration of the Molecular Exchange Process in Aqueous Solutions Using High-Resolution and Pulsed Field Gradient NMR Techniques","authors":"Svetlana V. Kurmaz, Ksenia V. Panicheva, Irina A. Avilova, Sergey G. Vasil’ev","doi":"10.1007/s00723-024-01744-x","DOIUrl":"10.1007/s00723-024-01744-x","url":null,"abstract":"<div><p>Water-soluble compositions of D-<i>α</i>-tocopherol (TP) as an effective antioxidant obtained by its encapsulation into amphiphilic copolymer of <i>N</i>-vinylpyrrolidone with hexyl methacrylate and triethylene glycol dimethacrylate (VP–HMA–TEGDM) and linear polyvinylpyrrolidone (PVP) were studied by electron absorption spectroscopy, dynamic light scattering and by <sup>1</sup>H high-resolution and pulsed field gradient (PFG) NMR. TP absorption band was at 292 nm in the absorption spectra of TP–VP–HMA–TEGDM and TP–PVP solutions, and the TP-loaded nanoparticles in water solution had average hydrodynamic radii, <i>R</i><sub>h</sub>, values about 65 and 57 nm, and diffusion coefficient, <i>D</i><sub>t</sub>, values were 3.7 × 10<sup>–8</sup> and 4.3 × 10<sup>–8</sup> cm<sup>2</sup>/s, respectively. The investigation of the self-diffusion by PFG NMR technique in addition reveals the presence of the phases of small sizes containing TP, which are invisible in DLS measurements. The investigation of the exchange between these phases shows that the retention time of TP in large associates is longer for TP–VP–HMA–TEGDM water solution compared to TP–PVP.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 4","pages":"499 - 519"},"PeriodicalIF":1.1,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00723-024-01744-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bruno H. Basso, Rodrigo H. S. Garcia, Milton A. Cardoso, Fábio R. Simões, Debora J. Moras, Esther R. D. Lima, Luiz A. Colnago, Lúcio L. Barbosa
{"title":"Using the Time-Domain Nuclear Magnetic Resonance (TD-NMR) for Quantification of the Diesel Adulteration with Ethanol","authors":"Bruno H. Basso, Rodrigo H. S. Garcia, Milton A. Cardoso, Fábio R. Simões, Debora J. Moras, Esther R. D. Lima, Luiz A. Colnago, Lúcio L. Barbosa","doi":"10.1007/s00723-024-01736-x","DOIUrl":"10.1007/s00723-024-01736-x","url":null,"abstract":"<div><p>Diesel is the most important liquid fuel in Brazil, representing 49.6% of the total liquid fuels commercialized in the country and, therefore, is important to have simple and rapid method for diesel quality control. The Brazilian National Agency of Petroleum, Gas and Biofuels verified that 4.0% of the diesel samples did not meet the required specification in 2022. Adulterated fuel increased fuel consumption, cause engine problems, increased emission of polluting gases among others problems. This study presents the use of bench top, time domain nuclear magnetic resonance (TD-NMR) relaxometer as a simple, rapid and non-destructive analytical method to quantify the adulteration of diesel with ethanol, which is the cheapest liquid fuel available in Brazil. The results show that commercial diesel and ethanol have transverse relaxation time (<i>T</i><sub>2</sub>) equal to 0.67 s and 1.75 s, respectively. The addition of 10–90% v/v) ethanol in diesel increased the <i>T</i><sub>2</sub> linearly. The correlation of <i>T</i><sub>2</sub> values with the middle infrared band at 1747 cm<sup>−1</sup> shows determination coefficient (<i>R</i><sup>2</sup> = 0.94). Therefore, TD-NMR relaxometry is a rapid, simple and alternative method to determine the adulteration of the commercial diesel with ethanol.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 4","pages":"441 - 452"},"PeriodicalIF":1.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143706983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Moamen Jbara, Oleg Zgadzai, Wolfgang Harneit, Aharon Blank
{"title":"Cryogenic W-band Electron Spin Resonance Probehead with an Integral Cryogenic Low Noise Amplifier","authors":"Moamen Jbara, Oleg Zgadzai, Wolfgang Harneit, Aharon Blank","doi":"10.1007/s00723-024-01732-1","DOIUrl":"10.1007/s00723-024-01732-1","url":null,"abstract":"<div><p>The quest to enhance the sensitivity of electron spin resonance (ESR) is an ongoing challenge. One potential strategy involves increasing the frequency, for instance, moving from Q-band (approximately 35 GHz) to W-band (approximately 94 GHz). However, this shift typically results in higher transmission and switching losses, as well as increased noise in signal amplifiers. In this work, we address these shortcomings by employing a W-band probehead integrated with a cryogenic low-noise amplifier (LNA) and a microresonator. This configuration allows us to position the LNA close to the resonator, thereby amplifying the acquired ESR signal with minimal losses. Furthermore, when operated at cryogenic temperatures, the LNA exhibits unparalleled noise levels that are significantly lower than those of conventional room temperature LNAs. We detail the novel probehead design and provide some experimental results at room temperature as well as cryogenic temperatures for representative paramagnetic samples. We find, for example, that spin sensitivity of ~ 3 × 10<sup>5</sup> spins/√Hz is achieved for a sample of phosphorus doped <sup>28</sup>Si, even for sub-optimal sample geometry with potential improvement to < 10<sup>3</sup> spins/√Hz in more optimal scenarios.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 1-2","pages":"265 - 284"},"PeriodicalIF":1.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00723-024-01732-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143108399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. V. Mamin, F. F. Murzakhanov, I. N. Gracheva, M. R. Gafurov, V. A. Soltamov
{"title":"Influence of Second-Order Effects due to Hyperfine Interaction on the Magnitude of the Larmor Frequency 14N","authors":"G. V. Mamin, F. F. Murzakhanov, I. N. Gracheva, M. R. Gafurov, V. A. Soltamov","doi":"10.1007/s00723-024-01733-0","DOIUrl":"10.1007/s00723-024-01733-0","url":null,"abstract":"<div><p>The negatively charged boron vacancy (<span>({text{V}}_{text{B}}^{-})</span>) in hexagonal boron nitride (hBN) is currently considered an intriguing quantum object for testing and developing quantum technologies on two-dimensional van der Waals materials. This article presents results from photoinduced electron spin echo (ESE)-detected electron spin resonance (ESR) and electron–nuclear double-resonance (ENDOR) spectroscopy at the W-band (ν = 94 GHz), focusing on the interactions of the <span>({text{V}}_{text{B}}^{-})</span> electron spin with the three nearest nitrogen nuclei (<sup>14</sup>N, <i>I</i> = 1). The lines in the ENDOR spectrum are due to both hyperfine and quadrupole interactions for <i>M</i><sub>S</sub> = ± 1 levels and only quadrupole interactions for <i>M</i><sub>S</sub> = 0 levels. We show that significant hyperfine interaction with the three nearest nitrogen atoms, despite the high magnetic field, results in a mixing of the hyperfine sublevels for <i>M</i><sub>S</sub> = 0. We show that significant hyperfine interaction with the three nearest nitrogen atoms, despite the high magnetic field, results in mixing of the hyperfine sublevels. This mixing shifts the <sup>14</sup>N Larmor frequency from its nominal value defined as <span>({{varvec{nu}}}_{{varvec{L}}}=boldsymbol{ }{{varvec{g}}}_{{varvec{N}}}{{varvec{mu}}}_{{varvec{N}}}{varvec{B}}/{varvec{h}})</span>. This shift observed through ENDOR experiments can be understood using spin-Hamiltonian formalism within the second-order perturbation theory. These findings enhance an understanding of electron–nuclear interactions in hBN.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 1-2","pages":"285 - 295"},"PeriodicalIF":1.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143108400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Automatic Skull Stripping Using Multidimensional Multi-input Multi-output U-Net Model for Alzheimer’s Disease","authors":"Priyanka Gautam, Manjeet Singh","doi":"10.1007/s00723-024-01737-w","DOIUrl":"10.1007/s00723-024-01737-w","url":null,"abstract":"<div><p>Skull stripping is a fundamental step in analyzing magnetic resonance imaging (MRI) scans, which play a crucial role in disease diagnosis such as Alzheimer’s disease (AD). Alzheimer’s is a progressive neurological disorder with no known cure. Early and precise diagnosis of AD is essential for timely intervention to help slow its progression. Although manual brain segmentation from MRI is accurate, it requires expert knowledge, experience, and time investment. Therefore, many automated brain segmentation algorithms have been introduced so far. The U-Net model has recently gained significant attention due to its exceptional volumetric medical image segmentation performance. This study presents a novel multidimensional multi-input multi-output U-Net (MIMO-U-Net) model for more efficient brain extraction. The model is multidimensional because it works with both 2D and 3D datasets. This architecture uses a dropout regularization technique with varying dropout rates across different layers. The concatenation connections are also used to combine high-level features with up-sampled output. The dropout regularization and concatenation help in enhancing the model performance. A refined loss function is also proposed by combining Dice loss and categorical focal loss. The MIMO-U-Net is trained and tested using a T1-weighted ADNI brain MRI dataset. The results indicate that MIMO-U-Net surpasses most existing techniques by offering better accuracy and notable quantitative and qualitative outcomes. In addition, the MIMO-U-Net showcases substantial computational efficiency during execution. Evaluation metrics, comprising the Dice coefficient, specificity, and sensitivity, corroborate the model’s performance with precise scores of 0.992, 0.999, and 0.995, respectively.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 4","pages":"453 - 480"},"PeriodicalIF":1.1,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143706934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kev M. Salikhov, Christiane R. Timmel, Eric J. L. McInnes, Gareth R. Eaton
{"title":"Preface to Special Issue Celebration of 80 Years of EPR Part 2","authors":"Kev M. Salikhov, Christiane R. Timmel, Eric J. L. McInnes, Gareth R. Eaton","doi":"10.1007/s00723-024-01738-9","DOIUrl":"10.1007/s00723-024-01738-9","url":null,"abstract":"","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 1-2","pages":"1 - 7"},"PeriodicalIF":1.1,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143108090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Saravanan, G. Arunkumar, T. Ragupathi, P. B. V. Raja Rao
{"title":"Weighted Majority Voting Ensemble for MRI-Based Brain Tumor Classification Using Capsule Networks and XGBoost","authors":"D. Saravanan, G. Arunkumar, T. Ragupathi, P. B. V. Raja Rao","doi":"10.1007/s00723-024-01731-2","DOIUrl":"10.1007/s00723-024-01731-2","url":null,"abstract":"<div><p>Brain Tumor (BT) is the most serious illness affecting humans, and its diagnosis is a complex process. Tumor location and type significantly affect treatment decisions, and survival rates improve with accurate identification and classification in the early stages. Magnetic Resonance Imaging (MRI) is mainly used for brain tumor analysis, but manual detection and classification by clinicians is challenging, often leading to high error rates, inaccurate diagnoses, and prolonged time requirements. To overcome these challenges, this paper introduces a novel hybrid classification approach that combines Capsule Networks (CapsNet) and XGBoost (XGB) to classify brain tumors from MRI images. The preprocessing step includes normalization, image blurring, resizing, contrast enhancement, and noise elimination, which are used to improve image quality. The classification process employs CapsNet to capture hierarchical features and spatial relationships in the images, while XGB utilizes extracted features, such as texture, intensity, and shape, to classify tumors effectively. To improve diagnostic accuracy, a Meta Ensemble Model combines the predictions of both algorithms using a Weighted Majority Voting approach, adjusting contributions based on each model’s confidence. Additionally, the Mantis Search Algorithm (MSA) is utilized for hyperparameter tuning, optimizing model performance by exploring the hyperparameter space effectively. The experiment assessed using the Brain Tumor MRI Dataset and Figshare Brain Tumor Dataset demonstrates the effectiveness of the proposed method, achieving an accuracy of 99.34% and a precision of 98.82%. These results indicate that the hybrid method is highly effective in accurately classifying various brain tumor types, which provides the best solution for clinical diagnostics.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 3","pages":"395 - 425"},"PeriodicalIF":1.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. N. Sashina, A. R. Khakimzyanova, A. M. Khakimov, A. V. Filippov, A. V. Khaliullina
{"title":"Structure and Mobility of the Lipid System in Mixtures of Ethylammonium Nitrate and Water: Magnetic Resonance Measurements and Molecular Dynamics Simulations","authors":"A. N. Sashina, A. R. Khakimzyanova, A. M. Khakimov, A. V. Filippov, A. V. Khaliullina","doi":"10.1007/s00723-024-01739-8","DOIUrl":"10.1007/s00723-024-01739-8","url":null,"abstract":"<div><p>Ionic liquids (ILs) are salts which persist in liquid state near room temperature. They are characterized by high thermal and chemical resistance, good solubility, and high ionic conductivity. ILs can be used as permeability enhancers for transdermal delivery of drugs. The study of the interaction of ILs with lipids is important for understanding their potential toxicity to cells and the environment. In this work, we discuss features of the molecular structure and mobility of the aqueous system consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and ethylammonium nitrate ionic liquid (EAN) mixtures studied by NMR and computer simulation MD methods. The <sup>31</sup>P NMR line shape analysis revealed two lipid states in the systems: in D<sub>2</sub>O it is a lamellar liquid crystalline state associated with the formed vesicle-like structures of DMPC, while in EAN it is isotopic. The ratio of these states correlates with the ratio of solvents in the system. Based on the self-diffusion coefficients obtained by NMR, sizes of the diffusing particles were estimated. The method of MD showed that DMPC molecules assemble into micelles in the presence of water. In the mixtures of EAN and water the configuration of DMPC molecules changed. When DMPC interacts only with EAN, the micelle disintegrates. It is thus inferred that the presence of IL in the environment significantly affects the structure of the lipid system. The comparative analysis of the SDCs revealed a correlation between values obtained by MD and NMR methods.</p></div>","PeriodicalId":469,"journal":{"name":"Applied Magnetic Resonance","volume":"56 4","pages":"481 - 498"},"PeriodicalIF":1.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00723-024-01739-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}