New Non-Invasive Method for the Authentication of Apple Cultivars.
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ABSTRACT:
SUBMITTER: Barberis E
PROVIDER: S-EPMC8750361 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:PurposeWe aimed at establishing a nomogram to accurately predict the overall survival (OS) of non-metastatic invasive micropapillary breast carcinoma (IMPC).MethodsIn the training cohort, data from 429 patients with non-metastatic IMPC were obtained through the Surveillance, Epidemiology, and End Results (SEER) database. Other 102 patients were enrolled at the Xijing Hospital as validation cohort. Independent risk factors affecting OS were ascertained using univariate and multivariate Cox regression. A nomogram was established to predict OS at 3, 5 and 8 years. The concordance index (C-index), the area under a receiver operating characteristic (ROC) curve and calibration curves were utilized to assess calibration, discrimination and predictive accuracy. Finally, the nomogram was utilized to stratify the risk. The OS between groups was compared through Kaplan-Meier survival curves.ResultsThe multivariate analyses revealed that race (p = 0.047), surgery (p = 0.003), positive lymph nodes (p = 0.027), T stage (p = 0.045) and estrogen receptors (p = 0.019) were independent prognostic risk factors. The C-index was 0.766 (95% CI, 0.682-0.850) in the training cohort and 0.694 (95% CI, 0.527-0.861) in the validation cohort. Furthermore, the predicted OS was consistent with actual observation. The AUCs for OS at 3, 5 and 8 years were 0.786 (95% CI: 0.656-0.916), 0.791 (95% CI: 0.669-0.912), and 0.774 (95% CI: 0.688-0.860) in the training cohort, respectively. The area under the curves (AUCs) for OS at 3, 5 and 8 years were 0.653 (95% CI: 0.498-0.808), 0.683 (95% CI: 0.546-0.820), and 0.716 (95% CI: 0.595-0.836) in the validation cohort, respectively. The Kaplan-Meier survival curves revealed a significant different OS between groups in both cohorts (p<0.001).ConclusionOur novel prognostic nomogram for non-metastatic IMPC patients achieved a good level of accuracy in both cohorts and could be used to optimize the treatment based on the individual risk factors.
| S-EPMC10369343 | biostudies-literature
Project description:Metabolome analyses by NMR spectroscopy can be used in quality control by generating unique fingerprints of different species. Hundreds of components and their variation between different samples can be analyzed in a few minutes/hours with high accuracy and low cost of sample preparation. Here, apple peel and pulp extracts of a variety of apple cultivars were studied to assess their suitability to discriminate between the different varieties. The cultivars comprised mainly newly bred varieties or ones that were brought onto the market in recent years. Multivariate analyses of peel and pulp extracts were able to unambiguously identify all cultivars, with peel extracts showing a higher discriminative power. The latter was increased if the highly concentrated sugar metabolites were omitted from the analysis. Whereas sugar concentrations lay within a narrow range, polyphenols, discussed as potential health promoting substances, and acids varied remarkably between the cultivars.
| S-EPMC5041128 | biostudies-literature
Project description:Early- to mid-season apple cultivars have recently been developed in response to global warming; however, their metabolite compositions remain unclear. Herein, metabolites, such as free sugars, and organic acids and antioxidant activity were determined in 10 new and 14 traditional apple cultivars. Additionally, the phenolic profiles of the apple pulp and peel were characterized by high-resolution mass spectrometry. Major phenolic compounds in apples varied depending on the cultivar and tissue (i.e., peel or pulp). Among the new apple cultivars, Decobell and Tinkerbell, showed high antioxidant activity and contained higher phenolic compound content than other cultivars in the peel and pulp, respectively. Honggeum showed high phenolic content with similar sugar to acid ratio compared to popular traditional cultivars. In addition to antioxidant phenolic contents, metabolite profile information can be used to select apple cultivars for various purposes. For example, Indo can be selected for sweet apple taste because of its higher sugar to acid ratio. This information can be used to select apple cultivars for various purposes. For example, Decobell peel could be used as sources of food supplements and food additives, and Tinkerbell pulp can be utilized for apple juice making according to its metabolite profile.
| S-EPMC7278836 | biostudies-literature
Project description:"Anna" is an early season apple cultivar exhibiting a fast softening and juiciness loss during storage, in comparison to two mid-late season cultivars "Galaxy" and "GD." The poor storage capacity of "Anna" was correlated with high lipid oxidation-related autoluminescence, high respiration and ethylene production rates, associated with high expression of MdACO1, 2, 4, 7, and MdACS1. All cultivars at harvest responded to exogenous ethylene by enhancing ethylene production, typical of system-II. The contribution of pre-climacteric events to the poor storage capacity of "Anna" was examined by comparing respiration and ethylene production rates, response to exogenous ethylene, expression of genes responsible for ethylene biosynthesis and response, and developmental regulators in the three cultivars throughout fruit development. In contrast to the "Galaxy" and "GD," "Anna" showed higher ethylene production and respiration rates during fruit development, and exhibited auto-stimulatory (system II-like) effect in response to exogenous ethylene. The higher ethylene production rate in "Anna" was correlated with higher expression of ethylene biosynthesis genes, MdACS3a MdACO2, 4, and 7 during early fruit development. The expression of negative regulators of ripening (AP2/ERF) and ethylene response pathway, (MdETR1,2 and MdCTR1) was lower in "Anna" in comparison to the other two cultivars throughout development and ripening. Similar pattern of gene expression was found for SQUAMOSA promoter binding protein (SBP)-box genes, including MdCNR and for MdFUL. Taken together, this study provides new understanding on pre-climacteric events in "Anna" that might affect its ripening behavior and physiology following storage.
| S-EPMC5591845 | biostudies-other
Project description:In recent decades, intensive selective breeding programs have allowed the development of disease-resistant and flavorsome apple cultivars while leading to a gradual decline of a large number of ancient varieties in many countries. However, the re-evaluation of such cultivars could lead to the production new apple-based products with health beneficial properties and/or unique flavor qualities. Herein, we report the comprehensive characterization of juices obtained from 86 old, mostly Danish, apple cultivars, by employing traditional analysis (ion chromatography, °Brix, headspace gas chromatography/mass spectrometry (GC-MS), and panel test evaluation) as well as an innovative nuclear magnetic resonance (NMR)-based screening method developed by Bruker for fruit juices, known as Spin Generated Fingerprint (SGF) Profiling™. Principal component analysis showed large differences in aroma components and sensory characteristics, including odd peculiar odors and flavors such as apricot and peach, and very different levels of phenolic compounds, acids and sugars among the analyzed juices. Moreover, we observed a tendency for late-season juices to be characterized by higher °Brix values, sugar content and they were perceived to be sweeter and more flavor intense than early-season juices. Our findings are useful for the production of specialty vintage-cultivar apple juices or mixed juices to obtain final products that are characterized both by healthy properties and peculiar sensory attributes.
| S-EPMC6680383 | biostudies-literature
Project description:BACKGROUND AND AIMS: It has been previously shown that abscission of apple fruitlets is preceded by an increase in ethylene evolution and in the amount of transcripts for 1-aminocyclopropane-1-carboxylate oxidase (ACO), an enzyme catalysing the final step in ethylene biosynthesis. These events are concomitant with shedding induction and chemical thinning. There are several thinners but their mode of action and efficacy is poorly understood. One of them is benzylaminopurine (BA), a cytokinin believed to act by enhancing vegetative activity and stressing the competition between shoots and fruitlets, thus leading to fruitlet shedding. Nevertheless, the specific mechanism of action of BA and the variable effect depending on apple cultivar (easy or difficult to thin) are poorly understood. METHODS: Abscission, the amount of MdACO1 transcripts and other parameters were followed in immature apple fruits during the period of physiological drop. The cultivars studied were 'Golden Delicious' and the 'spur' type 'Red Delicious'. BA was used as a thinning agent and was sprayed 14 d after petal fall (DAPF). Fruitlets were divided into central (C) and lateral (L) fruitlet populations. KEY RESULTS: Fruitlet size was significantly different between C and L fruitlets but it did not differ much between the populations within the same cultivar. C fruitlets were characterized by basal ethylene evolution while L fruitlets displayed an increase in hormone biosynthesis during abscission induction. Cluster composition evaluated by the L/C ratio differed in the two varieties, being almost unchanged throughout abscission induction in 'Golden Delicious' and progressively decreasing in 'Red Delicious'. Shoot growth activity evaluated at the end of the season indicated a possible connection with both the ongoing abscission and BA application. MDACO1 transcripts were mainly detected in L fruitlets and the accumulation was related to total abscission in 'Golden Delicious', while in 'Red Delicious' expression was observed in both C and L fruitlets. CONCLUSIONS: BA probably exerts its thinning effect through vegetative growth. In the 'spur' type 'Red Delicious' the chemical is ineffective, probably due to a limited action on shoot growth due to genetic characteristics. The amount of MdACO1 transcripts in seeds is a good indicator of abscission.
| S-EPMC3243580 | biostudies-literature
Project description:This research is focused on comparing the compositions of juice produced from old and commercially grown apple cultivars. We examined factors such as pH, total acids, soluble dry matter, polyphenol profile, and antioxidant activity, which impact the attributes, safety, shelf life, and nutritional value of the juice. Our analysis revealed differences between these two groups of cultivars. For instance, pH values ranged from 3.04 (in 'Bobovec') to 3.69 (in 'Fuji'). The proportions of acids varied from 0.07 g/100 mL (in 'Fuji') to 0.19 g/100 mL (in 'Wagener'). Soluble dry matter content ranged from 14.10% (in 'Fuji') to 18.50% (in 'Kraljevčica'). We also observed variations in sugar content and composition among cultivars; for example, sucrose levels varied from 16.11 g/L ('Fuji') to 39.36 g/L ('Golden Delicious). Glucose levels ranged from 4.95 g/L ('Jonagold') to 19.18 g/L ('Fuji'), while fructose levels spanned from 50.78 g/L ('Austrougarka') to 427.97 g/L ('Ilzer Rosenapfel'). Furthermore, old apple cultivars exhibited higher concentrations of phenols and flavonoids compared to commercial ones; we also noted significant variations in flavonol levels among different cultivars. The 'Wagener' and 'Božićnica' apple varieties had levels of myricetin measuring 0.53 and 0.52 µg/mL, respectively. On the other hand, 'Bobovec' stood out for its content of procyanidin B2 with a concentration of 422.61 µg/mL. When examining non-flavonoid compounds, it was found that old apple cultivars had higher concentrations of gallic acid, trans-ferulic acid, and chlorogenic acid. However, commercial cultivars showed dominance in caffeic and p-coumaric. Comparisons of antioxidant capacity using DPPH and ABTS assays clearly demonstrated the superiority of old apple cultivars. Overall, this study highlights the importance of utilizing apple cultivars for juice production. Their distinct compositions and higher antioxidant capacities contribute to potential health benefits. Preserving these cultivars for enhanced juice quality and nutritional value is encouraged. Further research could explore cultivation practices' impact on composition and health benefits.
| S-EPMC10650719 | biostudies-literature
Project description:We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.
2017-02-14 | GSE81194 | GEO
Project description:Arteriole and venule diameter ratio (A/V-ratio) can be measured using fundus photography. In this pilot study, we correlated changes in the intracranial pressure with the diameter of vessels of the retina. We investigated whether increased intracranial pressure (ICP) was reflected in a measurable and quantifiable distention of the venule diameter, leading to a decreased A/V-ratio. This was demonstrated by assessment of the A/V-ratio in patients already undergoing conventional ICP monitoring with a cerebral intraparenchymal pressure monitor. Our method shows a correlation between A/V ratio and ICP and suggests an easily obtainable and usable point-of-care (POC), non-invasive method to estimate the intracranial pressure without the necessity of mydriatic drugs. Furthermore, the sensitivity/specificity analysis with a cut-off of?<?0.8015 A/V-ratio, showed a sensitivity of 94% [85-98%] and a specificity of 50% [34-66%] with a positive likelihood ratio of 9.0. This means that in a clinical setting there is a 94% chance of correctly identifying individuals with ICP???20 mmHg.
| S-EPMC7400759 | biostudies-literature
Project description:Purpose: To find out the CT radiomics features of differentiating lung adenocarcinoma from another lung cancer histological type. Methods: This was a historical cohort study, three independent lung cancer cohorts included. One cohort was used to evaluate the stability of radiomics features, one cohort was used to feature selection, and the last was used to construct and evaluate classification models. The research is divided into four steps: region of interest segmentation, feature extraction, feature selection, and model building and validation. The feature selection methods included the intraclass correlation coefficient, ReliefF coefficient, and Partition-Membership filter. The performance metrics of the classification model included accuracy (Acc), precision (Pre), area under curve (AUC), and kappa statistics. Results: The 10 features (First order shape features: Sphericity and Compacity, Gray-Level Run Length Matrix: Short-Run Emphasis, Low Gray-level Run Emphasis, and High Gray-level Run Emphasis, Gray Level Co-occurrence Matrix: Homogeneity, Energy, Contrast, Correlation, and Dissimilarity) showed the most stable and classification capability. The 6 classifiers, Logistic regression classifier (LR), Sequence Minimum Optimization algorithm, Random Forest, KStar, Naive Bayes and Random Committee, have great performance both on the train and the test sets, and especially LR has the best performance on the test set (Acc = 98.72, Pre = 0.988, AUC = 1, and kappa = 0.974). Conclusion: Lung adenocarcinoma can be identified based on CT radiomics features. We can diagnose lung adenocarcinoma with CT non-invasively.
| S-EPMC7200977 | biostudies-literature