Because of its quantitative character and capability for high-throughput screening, 1H nuclear magnetic resonance (NMR) spectroscopy is used extensively in the profiling of biofluids such as urine ...and blood plasma. However, the narrow frequency bandwidth of 1H NMR spectroscopy leads to a severe overlap of the spectra of components present in the complex mixtures such as biofluids. Therefore, 1H NMR-based metabolomics analysis is focused on targeted studies related to concentrations of the small number of metabolites. Here, we propose a library-based approach to quantify proportions of overlapping metabolites from 1H NMR mixture spectra. The method boils down to the linear non-negative least squares (NNLS) problem, whereas proportions of the pure components contained in the library stand for the unknowns. The method is validated on an estimation of the proportions of (i) the 78 pure spectra, presumably related to type 2 diabetes mellitus (T2DM), from their synthetic linear mixture; (ii) metabolites present in 62 1H NMR spectra of urine of subjects with T2DM and 62 1H NMR spectra of urine of control subjects. In both cases, the in-house library of 210 pure component 1H NMR spectra represented the design matrix in the related NNLS problem. The proposed method pinpoints 63 metabolites that in a statistically significant way discriminate the T2DM group from the control group and 46 metabolites discriminating control from the T2DM group. For several T2DM-discriminative metabolites, we prove their presence by independent analytical determination or by pointing out the corresponding findings in the published literature.
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•Different pattern of the density distribution within pre-diabetic and diabetic liver.•The distribution of DAG composition dissimilar in pre-diabetic and diabetic liver.•The lipids ...species in the serum defined by MeV TOF-SIMS for the first time.•Serum analysis by MeV TOF-SIMS useful for in vivo investigation over time.
Hepatic insulin resistance, induced by fat, occurs before peripheral resistance and leads to prediabetes and diabetes. If insulin resistance is detected earlier, lifestyle changes could prevent or delay disease development. Therefore, we analysed lipids in the liver and serum of prediabetic and diabetic mice by MeV TOF-SIMS with a focus on diacylglycerols (DAGs) as the best predictor of (liver) resistance.
Glucose impairment was spontaneously developed or induced by HFD in NOD/LtJ mice, and prediabetic and diabetic mice were selected according to their glucose levels. MeV TOF-SIMS was applied to image the lipid distribution in the liver and to relatively quantify lipids related to insulin resistance in both the liver and serum.
The same lipids were detected in the liver and serum but with different intensities between mice. The intensity of DAGs and fatty acids was higher in the diabetic than that in the prediabetic liver.
Imaging of liver tissue showed a more compact density of prediabetic (non-fatty) than diabetic liver with DAG remodelling in diabetes. DAGs, which are greatly increased in diabetic serum, were successfully detected and quantified already in prediabetes.
MeV TOF-SIMS applied to the serum presents an excellent tool for in vivo monitoring of disease development over time.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Low-contrast images, such as color microscopic images of unstained histological specimens, are composed of objects with highly correlated spectral profiles. Such images are very hard to segment. ...Here, we present a method that nonlinearly maps low-contrast color image into an image with an increased number of non-physical channels and a decreased correlation between spectral profiles. The method is a proof-of-concept validated on the unsupervised segmentation of color images of unstained specimens, in which case the tissue components appear colorless when viewed under the light microscope. Specimens of human hepatocellular carcinoma, human liver with metastasis from colon and gastric cancer and mouse fatty liver were used for validation. The average correlation between the spectral profiles of the tissue components was greater than 0.9985, and the worst case correlation was greater than 0.9997. The proposed method can potentially be applied to the segmentation of low-contrast multichannel images with high spatial resolution that arise in other imaging modalities.
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We propose an offset-sparsity decomposition method for the enhancement of a color microscopic image of a stained specimen. The method decomposes vectorized spectral images into offset terms and ...sparse terms. A sparse term represents an enhanced image, and an offset term represents a "shadow." The related optimization problem is solved by computational improvement of the accelerated proximal gradient method used initially to solve the related rank-sparsity decomposition problem. Removal of an image-adapted color offset yields an enhanced image with improved colorimetric differences among the histological structures. This is verified by a no-reference colorfulness measure estimated from 35 specimens of the human liver, 1 specimen of the mouse liver stained with hematoxylin and eosin, 6 specimens of the mouse liver stained with Sudan III, and 3 specimens of the human liver stained with the anti-CD34 monoclonal antibody. The colorimetric difference improves on average by 43.86% with a 99% confidence interval (CI) of 35.35%, 51.62%. Furthermore, according to the mean opinion score, estimated on the basis of the evaluations of five pathologists, images enhanced by the proposed method exhibit an average quality improvement of 16.60% with a 99% CI of 10.46%, 22.73%.
A critical analysis was carried out for the purpose of understanding the role of subcolloidal (nanosized) (alumino)silicate precursor species in the early stage of crystallization of zeolites in ...heterogeneous systems (hydrogels). The formation and evolution of these subcolloidal species in both the solid and the liquid phases were investigated by various experimental methods such a scanning electron microscopy (SEM, FE-SEM), transmission electron microscopy, atomic force microscopy, particle size analysis, pH measurement, atomic absorption spectroscopy, and dynamic light scattering, after careful separation of intermediates from reaction mixture by two-step centrifugation treatment. The results revealed that a chain of processes (i) the formation of low-molecular-weight (LMW) silicate species, by dissolution of Al-enriched amorphous silica, and their aggregation into about 3 nm sized primary precursor species (PPSs), (ii) the formation of larger (∼3 to ∼15 nm sized) silicate precursor species (LSPSs) by a rapid aggregation/coalescence of PPSs, (iii) the formation of “gel” (primary amorphous precursor) by a random aggregation of LSPSs at room temperature, and (iv) the formation of the worm-like particles (secondary amorphous precursor) occurred in the solid phase during heating of the reaction mixture (hydrogel) from room temperature to 170 °C. It is interesting that almost the same processes occur in the liquid phase but with decreased rate according to the relative low concentration of LMW silicate species. With the above described findings, it is highly expected that the manipulation of crystallization pathway through controlling the formation/evolution of precursor species in the initial stage of the process can be achieved.
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•Publicly available dataset with 82 H&E stained images of frozen sections.•Images are acquired on 19 patients with metastatic colon cancer in a liver.•Pixel wise ground truths ...provided by seven domain experts.•Diagnostic results obtained with SVM, kNN, U-Net, U-Net++ and deeplabv3 classifiers.•Balanced accuracy and F1 score on independent test set amount to 89.34% and 83.67%.
The lack of pixel-wise annotated images severely hinders the deep learning approach to computer-aided diagnosis in histopathology. This research creates a public database comprised of: (i) a dataset of 82 histopathological images of hematoxylin-eosin stained frozen sections acquired intraoperatively on 19 patients diagnosed with metastatic colon cancer in a liver; (ii) corresponding pixel-wise ground truth maps annotated by four pathologists, two residents in pathology, and one final-year student of medicine. The Fleiss' kappa equal to 0.74 indicates substantial inter-annotator agreement; (iii) two datasets with images stain-normalized relative to two target images; (iv) development of two conventional machine learning and three deep learning-based diagnostic models. The database is available at http://cocahis.irb.hr. For binary, cancer vs. non-cancer, pixel-wise diagnosis we develop: SVM, kNN, U-Net, U-Net++, and DeepLabv3 classifiers that combine results from original images and stain-normalized images, which can be interpreted as different views. On average, deep learning classifiers outperformed SVM and kNN classifiers on an independent test set 14% in terms of micro balanced accuracy, 15% in terms of the micro F1 score, and 26% in terms of micro precision. As opposed to that, the difference in performance between deep classifiers is within 2%. We found an insignificant difference in performance between deep classifiers trained from scratch and corresponding classifiers pre-trained on non-domain image datasets. The best micro balanced accuracy estimated on the independent test set by the U-Net++ classifier equals 89.34%. Corresponding amounts of F1 score and precision are, respectively, 83.67% and 81.11%.
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Genetic variants of IL-18 and IL-12B may be important in immunoregulatory abnormalities, observed in the patients with Type 1 diabetes mellitus (T1DM), that contribute to individual differences in ...response to a treatment. Therefore, we examined the significance of IL-18-137G/C, IL-18-607C/A, and IL-12B A/C polymorphisms in Croatians (187 patients, 236 controls), not only as factors that contribute to susceptibility to T1DM, but also as determinants of the clinical presentation of disease.
The polymorphism screening has been performed using PCR sequence-specific primers (IL-18) or PCR-RFLP (IL-12B) approach. Results were evaluated by GraphPad Prism and Sigma Stat 3.5, Arlequin software and calculator for Hardy–Weinberg equilibrium.
The genotype, allele and haplotype distribution were not statistically different between the patients and control subjects. The clinical parameter analysis revealed that patients with minor alleles at each locus, IL-18-137C/-607A, were significantly younger at T1DM onset than carriers of major alleles, IL-18-137G/-607C (20 vs 23.5years). Moreover, the concomitant presence of minor alleles not only of IL-18 but also of IL-12B, is associated with the risk of disease progression even at younger age. These patients developed diabetes at 16years of age, what is significantly earlier (p=0.044) compared to 25.5years of age in patients with common alleles IL-18-137G/-607C/IL-12B A. Furthermore, combined genotype analysis of IL-18 and IL-12B has pointed out that patients with CC/AA/AA genotype have the worst glucose control based on HbA1c (8.7%, range 6.8–13.1%).
In conclusion, susceptibility to T1DM in Croatians is not strongly associated with IL-18-137/-607 and IL-12B polymorphisms. These SNPs are associated with the higher risk of earlier disease development and might be implicated in the effectiveness of glycemic control.
► We tested IL-18 (rs187238, rs1946518) and IL-12B (rs321227) SNPs in Type 1 diabetes. ► The minor alleles of both genes are associated with earlier diabetes development. ► Alleles of both genes are implicated in the effectiveness of glucose control (HbA1c). ► Tested SNPs of IL-18/IL-12B genes could determine the clinical outcome in patients.
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This study aimed at evaluating the efficacy of oral treatment and skin decontamination with the mineral cationic carrier in sarin-intoxicated mice. Mice were contaminated with increasing percutaneous ...sarin doses and decontaminated. Furthermore, the surviving mice were treated per os. The behavioral patterns of the surviving animals were monitored for 72 h, including the animals' posture, desire for food and water, and approach and touch response. The results showed the mineral cationic carrier to be capable of efficiently decontaminating animals percutaneous poisoned with triple lethal dose. The comparison of behavioral pattern of control animals against those treated per os showed statistically significant differences. Oral treatment with mineral cationic carrier may be a detoxification tool against nerve agents' poisoning, and this merits further research.
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A methodology is proposed for nonlinear contrast-enhanced unsupervised segmentation of multispectral (color) microscopy images of principally unstained specimens. The methodology exploits spectral ...diversity and spatial sparseness to find anatomical differences between materials (cells, nuclei, and background) present in the image. It consists of r th-order rational variety mapping (RVM) followed by matrix/tensor factorization. Sparseness constraint implies duality between nonlinear unsupervised segmentation and multiclass pattern assignment problems. Classes not linearly separable in the original input space become separable with high probability in the higher-dimensional mapped space. Hence, RVM mapping has two advantages: it takes implicitly into account nonlinearities present in the image (ie, they are not required to be known) and it increases spectral diversity (ie, contrast) between materials, due to increased dimensionality of the mapped space. This is expected to improve performance of systems for automated classification and analysis of microscopic histopathological images. The methodology was validated using RVM of the second and third orders of the experimental multispectral microscopy images of unstained sciatic nerve fibers (nervus ischiadicus) and of unstained white pulp in the spleen tissue, compared with a manually defined ground truth labeled by two trained pathophysiologists. The methodology can also be useful for additional contrast enhancement of images of stained specimens.
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