The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four ...representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.
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IJS, NUK, SBMB, UL, UM, UPUK
Abstract Background Neuroinflammation has been proven to play a crucial role in early brain injury pathogenesis and represents a target for treatment of subarachnoid hemorrhage (SAH). Astaxanthin ...(ATX), a dietary carotenoid, has been shown to have powerful anti-inflammation property in various models of tissue injury. However, the potential effects of ATX on neuroinflammation in SAH remain uninvestigated. The goal of this study was to investigate the protective effects of ATX on neuroinflammation in a rat prechiasmatic cistern SAH model. Methods Rats were randomly distributed into multiple groups undergoing the sham surgery or SAH procedures, and ATX (25 mg/kg or 75 mg/kg) or equal volume of vehicle was given by oral gavage at 30 min after SAH. All rats were sacrificed at 24 h after SAH. Neurologic scores, brain water content, blood–brain barrier permeability, and neuronal cell death were examined. Brain inflammation was evaluated by means of expression changes in myeloperoxidase, cytokines (interleukin-1β, tumor necrosis factor-α), adhesion molecules (intercellular adhesion molecule-1), and nuclear factor kappa B DNA-binding activity. Results Our data indicated that post-SAH treatment with high dose of ATX could significantly downregulate the increased nuclear factor kappa B activity and the expression of inflammatory cytokines and intercellular adhesion molecule-1 in both messenger RNA transcription and protein synthesis. Moreover, these beneficial effects lead to the amelioration of the secondary brain injury cascades including cerebral edema, blood–brain barrier disruption, neurological dysfunction, and neuronal degeneration. Conclusions These results indicate that ATX treatment is neuroprotective against SAH, possibly through suppression of cerebral inflammation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Current machine learning techniques provide the opportunity to develop noninvasive and automated glioma grading tools, by utilizing quantitative parameters derived from multi-modal magnetic resonance ...imaging (MRI) data. However, the efficacies of different machine learning methods in glioma grading have not been investigated.A comprehensive comparison of varied machine learning methods in differentiating low-grade gliomas (LGGs) and high-grade gliomas (HGGs) as well as WHO grade II, III and IV gliomas based on multi-parametric MRI images was proposed in the current study. The parametric histogram and image texture attributes of 120 glioma patients were extracted from the perfusion, diffusion and permeability parametric maps of preoperative MRI. Then, 25 commonly used machine learning classifiers combined with 8 independent attribute selection methods were applied and evaluated using leave-one-out cross validation (LOOCV) strategy. Besides, the influences of parameter selection on the classifying performances were investigated. We found that support vector machine (SVM) exhibited superior performance to other classifiers. By combining all tumor attributes with synthetic minority over-sampling technique (SMOTE), the highest classifying accuracy of 0.945 or 0.961 for LGG and HGG or grade II, III and IV gliomas was achieved. Application of Recursive Feature Elimination (RFE) attribute selection strategy further improved the classifying accuracies. Besides, the performances of LibSVM, SMO, IBk classifiers were influenced by some key parameters such as kernel type, c, gama, K, etc. SVM is a promising tool in developing automated preoperative glioma grading system, especially when being combined with RFE strategy. Model parameters should be considered in glioma grading model optimization.
Background
Accurate glioma grading plays an important role in patient treatment.
Purpose
To investigate the influence of varied texture retrieving models on the efficacy of grading glioma with ...support vector machine (SVM).
Study Type
Retrospective.
Population
In all, 117 glioma patients including 25, 29, and 63 grade II, III, and IV gliomas, respectively, based on WHO 2007.
Field Strength/Sequence
3.0T MRI/ T1WI, T2 fluid‐attenuated inversion recovery, contrast enhanced T1, arterial spinal labeling, diffusion‐weighted imaging (0, 30, 50, 100, 200, 300, 500, 800, 1000, 1500, 2000, 3000, and 3500 sec/mm2), and dynamic contrast‐enhanced.
Assessment
Texture attributes from 30 parametric maps were retrieved using four models, including Global, gray‐level co‐occurrence matrix (GLCM), gray‐level run‐length matrix (GLRLM), and gray‐level size‐zone matrix (GLSZM). Attributes derived from varied models were input into radial basis function SVM (RBF‐SVM) combined with attribute selection using SVM‐recursive feature elimination (SVM‐RFE). The SVM model was trained and established with 80% randomly selected data of each category using 10‐fold crossvalidation. The model performance was further tested using the remaining 20% data.
Statistical Tests
Ten‐fold crossvalidation was used to validate the model performance.
Results
Based on 30 parametric maps, 90, 240, 390, or 390 texture attributes were retrieved using the Global, GLCM, GLRLM, or GLSZM model, respectively. SVM‐RFE was able to reduce attribute redundancy as well as improve RBF‐SVM performance. Training data were oversampled by applying the Synthetic Minority Oversampling Technique (SMOTE) method to overcome the data imbalance problem; test results were able to further demonstrate the classifying performance of the final models. GLSZM using gray‐level 64 was the optimal model to retrieve powerful image texture attributes to produce enough classifying power with an accuracy / area under the curve of 0.760/0.867 for the training and 0.875/0.971 for the independent test. Fifteen attributes were selected with SVM‐RFE to provide comparable classifying efficacy.
Data Conclusion
When using image textures‐based SVM classification of gliomas, the GLSZM model in combination with gray‐level 64 and attribute selection may be an optimized solution.
Level of Evidence: 2
Technical Efficacy: Stage 2
J. Magn. Reson. Imaging 2019;49:1263–1274.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Principal component analysis network (PCANet), as an unsupervised shallow network, demonstrates noticeable effectiveness on datasets of various volumes. It carries a two-layer convolution with PCA as ...filter learning method, followed by a block-wise histogram post-processing stage. Following the structure of PCANet, extreme learning machine auto-encoder (ELM-AE) variants are employed to replace the PCA’s role, which come from extreme learning machine network (ELMNet) and hierarchical ELMNet. ELMNet emphasizes the importance of orthogonal projection while overlooking non-linearity. The latter introduces complex pre-processing to overcome drawback of non-linear ELM-AE. In this paper, we analyze intrinsic characteristics of ELM-AE variants and accordingly propose a regularized ELM-AE, which combines non-linearity learning capability and approximately orthogonal projection. Experiments on image classification show the effectiveness compared to supervised convolutional neural networks and related shallow networks on unsupervised feature learning.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The methylation status of oxygen 6-methylguanine-DNA methyltransferase (MGMT) promoter has been associated with treatment response in glioblastoma(GBM). Using pre-operative MRI techniques to predict ...MGMT promoter methylation status remains inconclusive. In this study, we investigated the value of features from structural and advanced imagings in predicting the methylation of MGMT promoter in primary glioblastoma patients.
Ninety-two pathologically confirmed primary glioblastoma patients underwent preoperative structural MR imagings and the efficacy of structural image features were qualitatively analyzed using Fisher's exact test. In addition, 77 of the 92 patients underwent additional advanced MRI scans including diffusion-weighted (DWI) and 3-diminsional pseudo-continuous arterial spin labeling (3D pCASL) imaging. Apparent diffusion coefficient (ADC) and relative cerebral blood flow (rCBF) values within the manually drawn region-of-interest (ROI) were calculated and compared using independent sample t test for their efficacies in predicting MGMT promoter methylation. Receiver operating characteristic curve (ROC) analysis was used to investigate the predicting efficacy with the area under the curve (AUC) and cross validations. Multiple-variable logistic regression model was employed to evaluate the predicting performance of multiple variables.
MGMT promoter methylation was associated with tumor location and necrosis (P < 0.05). Significantly increased ADC value (P < 0.001) and decreased rCBF (P < 0.001) were associated with MGMT promoter methylation in primary glioblastoma. The ADC achieved the better predicting efficacy than rCBF (ADC: AUC, 0.860; sensitivity, 81.1%; specificity, 82.5%; vs rCBF: AUC, 0.835; sensitivity, 75.0%; specificity, 78.4%; P = 0.032). The combination of tumor location, necrosis, ADC and rCBF resulted in the highest AUC of 0.914.
ADC and rCBF are promising imaging biomarkers in clinical routine to predict the MGMT promoter methylation in primary glioblastoma patients.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
2D ferromagnets, such as CrX
3
(X = Cl, Br and I), have been attracting extensive attention since they provide novel platforms to fundamental physics and device applications. Integrating CrX
3
with ...other electrodes and substrates is an essential step to their device realization. Therefore, it is important to understand the interfacial properties between CrX
3
and other 2D materials. As an illustrative example, we have investigated the heterostructures between CrX
3
and graphene (CrX
3
/Gr) by first-principles calculations. We found a unique Schottky contact type with strongly spin-dependent barriers in CrX
3
/Gr. This can be understood by synergistic effects between the exchange splitting of the semiconductor band of CrX
3
and interlayer charge transfer. The spin-asymmetry of Schottky barriers may result in different tunneling rates of spin-up and down electrons, and then lead to spin-polarized current, namely the spin-filter (SF) effect. Moreover, by introducing X vacancies into CrX
3
/Gr, an ohmic contact forms in the spin-up direction. It may enhance the transport of spin-up electrons, and improve the SF effect. Our systematic study reveals the unique interfacial properties of CrX
3
/Gr, and provides a theoretical view of the understanding and designing of spintronic devices based on magnetic vdW heterostructures.
The Schottky barriers are spin-dependent in magnetic vdW heterostructures.
Due to lower farrowing rate and reduced litter size with frozen-thawed semen, over 90% of artificial insemination (AI) is conducted using liquid stored boar semen. Although substantial progress has ...been made towards optimizing the cryopreservation protocols for boar sperm, the influencing factors and underlying mechanisms related to cryoinjury and freeze tolerance of boar sperm remain largely unknown. In this study, we report the differential expression of mRNAs and miRNAs between fresh and frozen-thawed boar sperm using high-throughput RNA sequencing. Our results showed that 567 mRNAs and 135 miRNAs were differentially expressed (DE) in fresh and frozen-thawed boar sperm. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the majority of DE mRNAs were enriched in environmental information processing such as cytokine-cytokine receptor interactions, PI3K-Akt signaling, cell adhesion, MAPK, and calcium signaling pathways. Moreover, the targets of DE miRNAs were enriched in significant GO terms such as cell process, protein binding, and response to stimuli. In conclusion, we speculate that DE mRNAs and miRNAs are heavily involved in boar sperm response to environment stimuli, apoptosis, and metabolic activities. The differences in expression also reflect the various structural and functional changes in sperm during cryopreservation.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
A feeding trial was conducted to determine the amount of soybean meal (SBM) that could replace fish meal (FM) without compromising growth and health of Asian red‐tailed catfish (Hemibagrus ...wyckioides). Five isonitrogenous and isoenergetic diets (S0, S15, S30, S45 and S60) were formulated with SBM to replace 0%, 15%, 30%, 45% and 60% of FM. The replacement level up to 30% improved daily growth coefficient, plasma adenosine monophosphate deaminase (AMPD) and alanine aminotransferase (ALT) activities and IgM content, and hepatic ALT, aspartate aminotransferase (AST) and glutathione reductase activities, whereas these were depressed by a further inclusion. The highest protein efficiency ratio and lowest feed conversion ratio were observed in fish fed the S15 diet. Replacement of FM with SBM generally decreased plasma insulin and insulin‐like growth factor 1 (IGF‐1) contents and hepatic catalase activity, whereas no significant differences were observed among fish fed the S0, S15 and S30 diets. In contrast, replacing FM with SBM generally increased blood urea nitrogen content, and that was higher in fish fed the S60 diet compared to fish fed the S0 diet. The highest growth hormone (GH) and glutamate dehydrogenase (GDH) activities were observed in fish fed the S30 diet. Fish fed the S30 and S45 diets exhibited the highest hepatic AMPD, GDH, IGF‐1 and target of rapamycin mRNA levels and muscle AMPD and GDH mRNA levels, whereas those were lowest in fish fed the S60 diet. These results indicate that under the reported conditions SBM may be included in the diet up to 222 g/kg as a substitute for FM, replacing about 30% of FM protein in juvenile H. wyckioides.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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