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result(s) for
"Cui, Fa"
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MRI-Based radiomics nomogram for differentiation of benign and malignant lesions of the parotid gland
2021
Objectives
Preoperative differentiation between benign parotid gland tumors (BPGT) and malignant parotid gland tumors (MPGT) is important for treatment decisions. The purpose of this study was to develop and validate an MRI-based radiomics nomogram for the preoperative differentiation of BPGT from MPGT.
Methods
A total of 115 patients (80 in training set and 35 in external validation set) with BPGT (
n
= 60) or MPGT (
n
= 55) were enrolled. Radiomics features were extracted from T1-weighted and fat-saturated T2-weighted images. A radiomics signature model and a radiomics score (Rad-score) were constructed and calculated. A clinical-factors model was built based on demographics and MRI findings. A radiomics nomogram model combining the Rad-score and independent clinical factors was constructed using multivariate logistic regression analysis. The diagnostic performance of the three models was evaluated and validated using ROC curves on the training and validation datasets.
Results
Seventeen features from MR images were used to build the radiomics signature. The radiomics nomogram incorporating the clinical factors and radiomics signature had an AUC value of 0.952 in the training set and 0.938 in the validation set. Decision curve analysis showed that the nomogram outperformed the clinical-factors model in terms of clinical usefulness.
Conclusions
The above-described radiomics nomogram performed well for differentiating BPGT from MPGT, and may help in the clinical decision-making process.
Key Points
•
Differential diagnosis between BPGT and MPGT is rather difficult by conventional imaging modalities.
•
A radiomics nomogram integrated with the radiomics signature, clinical data, and MRI features facilitates differentiation of BPGT from MPGT with improved diagnostic efficacy.
Journal Article
Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat
2023
The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture, but the involvement of epigenetic modifications remains unexplored. Here, we analyze the chromatin landscapes of two wheat cultivars (KN9204 and J411) that differ in NUE under varied nitrogen conditions. The expression of nitrogen metabolism genes is closely linked to variation in histone modification instead of differences in DNA sequence. Epigenetic modifications exhibit clear cultivar-specificity, which likely contributes to distinct agronomic traits. Additionally, low nitrogen (LN) induces H3K27ac and H3K27me3 to significantly enhance root growth in KN9204, while remarkably inducing
NRT2
in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of H3K27me3 methyltransferase shows that changes in epigenetic modifications could alter the strategy preference for root development or nitrogen uptake in response to LN. Here, we show the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.
The analysis of wheat cultivars reveals that variations in histone modification, rather than DNA sequence, are closely linked to the expression of nitrogen metabolism genes and distinct agronomic traits. The findings suggest that epigenetic regulation plays a crucial role in cultivar-specific adaptation to low nitrogen conditions in wheat.
Journal Article
Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number
2017
In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.
Journal Article
Serum sST2, IL-33, and Hcy Expression in Older Adults Patients with Myocardial Infarction and Their Predictive Value for MACE
2025
Acute myocardial infarction (AMI) in the elderly is associated with high morbidity and mortality, with major adverse cardiovascular events (MACE) remaining a major concern despite early revascularization. This study aimed to evaluate the association of soluble suppression of tumorigenicity 2 (sST2), interleukin-33 (IL-33), and homocysteine (Hcy) with coronary stenosis severity and their predictive value for MACE in elderly AMI patients.
A retrospective analysis was conducted on 143 elderly AMI patients (≥65 years) admitted between June 2022 and June 2024. Patients were divided into two groups based on MACE occurrence: Group A (no MACE, n=56) and Group B (MACE, n=87). Serum sST2, IL-33, and Hcy levels were measured using ELISA, and coronary stenosis severity was assessed using the Gensini score. Statistical analyses included Spearman correlation, multivariate logistic regression, and receiver operating characteristic (ROC) curve analysis to evaluate predictive performance.
Serum sST2, IL-33, and Hcy levels were significantly higher in the MACE group compared to the non-MACE group (72.37±10.68 vs 38.76±11.15, p<0.05; 60.61±10.89 vs 33.74±11.23, p<0.05; 32.76±4.15 vs 15.38±4.62, p<0.05, respectively). Biomarker levels positively correlated with coronary stenosis severity (sST2: r=0.647, p<0.05; IL-33: r=0.659, p<0.05; Hcy: r=0.582, p<0.05). Multivariate logistic regression confirmed that sST2 (OR=1.056, 95% CI: 1.015-1.094, p=0.005), IL-33 (OR=1.069, 95% CI: 1.024-2.016, p=0.001), and Hcy (OR=1.037, 95% CI: 1.008-1.077, p=0.033) were independent risk factors for MACE. ROC analysis showed that sST2, IL-33, and Hcy had AUCs of 0.841 (95% CI: 0.762-0.915, p<0.001), 0.803 (95% CI: 0.724-0.878, p<0.001), and 0.729 (95% CI: 0.642-0.812, p<0.001), respectively. Combined detection of all three biomarkers significantly improved MACE prediction (AUC=0.910, 95% CI: 0.851-0.956, p<0.001).
Serum sST2, IL-33, and Hcy levels are positively correlated with coronary stenosis severity and independently associated with MACE in elderly AMI patients. Their combined detection significantly enhances MACE prediction, providing a potential strategy for improved risk stratification and management in this high-risk population.
Journal Article
Dissection of Pleiotropic QTL Regions Controlling Wheat Spike Characteristics Under Different Nitrogen Treatments Using Traditional and Conditional QTL Mapping
2019
Optimal spike characteristics are critical in improving the sink capacity and yield potential of wheat even in harsh environments. However, the genetic basis of their response to nitrogen deficiency is still unclear. In this study, quantitative trait loci (QTL) for six spike-related traits, including heading date (HD), spike length (SL), spikelet number (SN), spike compactness (SC), fertile spikelet number (FSN), and sterile spikelet number (SSN), were detected under two different nitrogen (N) supplies, based on a high-density genetic linkage map constructed by PCR markers, DArTs, and Affymetrix Wheat 660 K SNP chips. A total of 157 traditional QTLand 54 conditional loci were detected by inclusive composite interval mapping, among which three completely low N-stress induced QTL for SN and FSN (
, and
) were found to maintain the desired spikelet fertility and kernel numbers even under N deficiency through pyramiding elite alleles. Twenty-eight stable QTL showing significant differencet in QTL detection model were found and seven genomic regions (R2D, R4A, R4B, R5A, R7A, R7B, and R7D) clustered by these stable QTL were highlighted. Among them, the effect of R4B on controlling spike characteristics might be contributed from
. R7A harboring three major stable QTL (
, and
) might be one of the valuable candidate regions for further genetic improvement. In addition, the R7A was found to show syntenic with R7B, indicating the possibly exsting homoeologous candidate genes in both regions. The SNP markers involved with the above highlighted regions will eventually facilitate positional cloning or marker-assisted selection for the optimal spike characteristics under various N input conditions.
Journal Article
Editorial: Genetic improvement of Triticeae crops based on high-throughput phenotyping: Molecular design for yield, resistance and tolerance
by
Liu, Shuyu
,
Cui, Fa
,
Fan, Xiaoli
in
Abiotic stress
,
Agricultural production
,
Airborne microorganisms
2023
In addition to powdery mildew, resistance to other destructive diseases, such as leaf rust and stem rust, were also presented.Zhang et al.applied 112 wheat accessions introduced from the U.S. National Plant Germplasm System to evaluate resistance to the Chinese predominant races causing leaf rust and their resistance genes in order to explore more effective resistance resources for overcoming wheat leaf rust.Kataria and Kaundalperformed a comparative analysis of protein-protein interactions (PPIs) between two pathogen races, Pgt 21-0 and Pgt Ug99, both causing wheat stem rust, and elucidated the functional differences between these two races, thus providing the strain-specific information for the development of durable, disease-resistant crop lines. Abiotic stress response in Triticeae crops Natural cultivation conditions, such as light, nutrients, water, and salinity, determine crop adaptability and affect their yield and quality.Yang et al.discovered that low-light stressed wheat could alter its pollination type to enable outcrossing with heterologous pollen by increasing lemma and glume angles, which finally compensated for the 2.1–18.0% loss in grain number.Liu et al.analyzed the transcriptional mechanism of the response to low-nitrogen stress of a previously located major stable QTL for wheat root growth, QMrl-7B, and found genes encoding NO3- transporters, etc, composing the complex regulatory network for root determination.Li et al.also performed the transcriptome profiling of the well-known transcription factor gene family, WRKYs, in Tritiprum and the response of TtWRKY256 to salt stress. [...]considering that the chlorophyll content could directly impact photosynthesis and affect crop health,Wang et al.proposed an unmanned aerial vehicle (UAV)-based approach to rapidly and efficiently predict chlorophyll content under irrigation and drought stress to provide insights into the capacity of UAV-based remote sensing for phenotyping to improve crop breeding. Yield-related trait response to stresses in Triticeae crops Maintaining yield performance under various unfavorable conditions is the main concern for breeders during genetic improvement of resistance or tolerance to both biotic and abiotic stresses (Deng et al., 2017).Wang et al.studied a set of 18 yield-related and agronomic traits in wheat under different irrigation regions by QTL analysis to provide insight into the genomic regions contributing to high yield in water-limited conditions and reported a novel QTL stably controlling wheat kernel length under all tested environments, facilitating the future MAS for pyramiding the favorable loci for high-yield improvement.Zhang et al.identified three QTLs for wheat spikelet nodes per spike and investigated incorporation of their favorable alleles across different wheat agroecological production zones of China, such as Chengdu of the Southwestern Wheat Zone and Yuncheng and Linfen of the Huai River Valleys Facultative Wheat Zone, where the natural environmental factors were significantly different, advancing our understanding of the genetic basis of natural variation in spikelet development and its adaptation to environmental change.
Journal Article
Characterization of a wheat stable QTL for spike length and its genetic effects on yield-related traits
2024
Spike length (SL) is one of the most important agronomic traits affecting yield potential and stability in wheat. In this study, a major stable quantitative trait locus (QTL) for SL, i.e.,
qSl-2B
, was detected in multiple environments in a recombinant inbred line (RIL) mapping population, KJ-RILs, derived from a cross between Kenong 9204 (KN9204) and Jing 411 (J411). The
qSl-2B
QTL was mapped to the 60.06–73.06 Mb region on chromosome 2B and could be identified in multiple mapping populations. An InDel molecular marker in the target region was developed based on a sequence analysis of the two parents. To further clarify the breeding use potential of
qSl-2B
, we analyzed its genetic effects and breeding selection effect using both the KJ-RIL population and a natural mapping population, which consisted of 316 breeding varieties/advanced lines. The results showed that the
qSl-2B
alleles from KN9204 showed inconsistent genetic effects on SL in the two mapping populations. Moreover, in the KJ-RILs population, the additive effects analysis of
qSl-2B
showed that additive effect was higher when both
qSl-2D
and
qSl-5A
harbor negative alleles under LN and HN. In China, a moderate selection utilization rate for
qSl-2B
was found in the Huanghuai winter wheat area and the selective utilization rate for
qSl-2B
continues to increase. The above findings provided a foundation for the genetic improvement of wheat SL in the future via molecular breeding strategies.
Key message
A major stable QTL for spike length was identified in wheat, and its genetic effect on yield related-traits as well as its potential use value in molecular breeding programs were characterized.
Journal Article
The Circadian Clock Gene, TaPRR1, Is Associated With Yield-Related Traits in Wheat (Triticum aestivum L.)
by
Wu, Yongzhen
,
Cui, Fa
,
Jia, Jizeng
in
Agricultural production
,
association analysis
,
Biological clocks
2020
Timing of flowering is crucial for the transformation from vegetative to reproductive growth in the important food crop, wheat (
L.). The circadian clock is a central part of photoperiod regulation, with Pseudo-Response Regulators (PRRs) representing key components of circadian networks. However, little is known about the effects of PRR family members on yield-related traits in crop plants. In this study, we identified polymorphisms and haplotypes of
, demonstrating that natural variations in
are associated with significant differences in yield-related traits including heading date, plant height and thousand grain weight.
showed an earlier heading date, advanced by 0.9 to 1.7%.
and
displayed reduced plant height and increased thousand grain weight of up to 13.3 to 26.4% and 6.3 to 17.3%, respectively. Subcellular localization and transcriptional activity analysis showed that TaPRR1 is a nuclear localization protein with transcriptional activity controlled by an IR domain. The expression profiles of
genes over a 48-h period were characterized by circadian rhythms, which had two peaks under both short- and long- day conditions. In addition, geographical distribution analysis indicated higher distribution frequencies of
,
, and
in different agro-ecological production zones. Furthermore, analysis of molecular variance of the distribution frequency of
haplotypes suggested significant differences in haplotype distribution frequency between landraces and modern cultivars. Our study provides a basis for in-depth understanding of
function on yield-related traits in wheat, as well as establishing theoretical guidance for wheat molecular marker-assisted breeding.
Journal Article
Primary spinal epidural abscess: magnetic resonance imaging characteristics and diagnosis
2024
Rationale and objective
To investigate the MR characteristics of phlegmonous stage and abscess stage primary spinal epidural abscess.
Materials and methods
This study retrospectively analyzed the clinical and imaging characteristics of 27 cases of pathologically confirmed primary spinal epidural abscess. Predisposing conditions of all patients were collected. All patients underwent conventional magnetic resonance imaging, while fifteen patients also underwent post-contrast magnetic resonance imaging.
Results
The initial symptoms included back pain in 25 patients, fever in 18, motor deficit in five, and sensory changes in 13. Underlying diseases included distant site of infection in seven, injection therapy in five, neoplasm in five, chronic inflammatory disease in five, diabetes mellitus in four, alcoholism in three, metabolic disorder in three, hepatopathy in three, and obesity in two. Abscess location was ventral epidural space in 15 patients (55.6%) and dorsal epidural space in 12 (44.4%). On T1-weighted image, the abscess was hypointense to the spinal cord in 23 patients (85%) and isointense in four (15%). All abscesses were hyperintense to the spinal cord on T2-weighted image. Among the 15 patients who underwent contrast-enhanced imaging, ring enhancement was present in 13 and homogeneous enhancement in two. Adjacent vertebrae body edema was present in four patients. The abscess was purely intraspinal in 25 patients (92.6%). Paraspinal extension was present in two (7.4%).
Conclusion
Primary spinal epidural abscess patients have one or more predisposing conditions. Phlegmonous stage primary spinal epidural abscess appears isointense on T1WI and hyperintense on T2WI and enhancement is homogeneous. Abscess stage primary spinal epidural abscess hyperintense on T2WI and hypointense on T1WI and ring enhancement. Presence of vertebral body edema is an important sign to help diagnose primary spinal epidural abscess.
Journal Article
Quantitative trait locus mapping for salt and drought tolerance traits in wheat (Triticum aestivum L.)
2025
Background
Wheat (
Triticum aestivum
L.) is susceptible to abiotic factors during its growth period, such as salt and drought. The germination stage is the initial growth stage of wheat growth, when wheat is particularly sensitive to salt and drought stress.
Results
In this study, the genetic basis of salt and drought tolerance in wheat was explored using a recombinant inbred lines (RILs) population consisting of 188 lines derived from a cross between the cultivars Kenong9204 (KN9204) and Jing411 (J411). The KJ-RIL lines and their parents were evaluated under 100 mM NaCl salt stress and 10% polyethylene glycol 6000 (PEG-6000) induced drought stress. A principal component analysis (PCA) showed that the cumulative contribution rate of the four principal components was 87.16% and 85.62% under salt and drought stress, respectively. A total of 16 salt-tolerant and five drought-tolerant lines were selected using the membership function and 52 putative additive quantitative trait loci (QTLs) and 251 epistatic QTLs (eQTLs) for eight traits were detected in the KJ-RILs. Among the 251 eQTLs, 19, 32, 67, 21, 27, 29, 32, and 24 pairwise eQTLs were observed for sheath length, seedling length, maximum root length, root number, seedling fresh weight, root fresh weight, seedling dry weight, and root dry weight, respectively. The 52 putative additive QTLs were found in all of the 21 wheat chromosomes except 1A, 2D, and 4A. The QTLs accounted for 3.92–13.26% of the phenotypic variation with logarithm of the odds values ranging from 2.52–6.91. A total of seven stable QTLs were detected:
qShl-1D
,
qShl-3B
,
qSl-4D
,
qMrl-1D
,
qRn-2A.3
,
qRn-4B
, and
qRdw-7D
, and three major QTLs were detected:
qShl-4B
,
qRn-3B
, and
qRfw-7D
. Among them,
qShl-3B
was a stable major QTL that explained 10.96%–12.02% of the variation rate and the most favorable allele came from KN9204. In addition, an InDel marker closely linked to
qShl-3B
was developed and validated in 188 RILs.
Conclusion
Different putative additive QTLs and epistatic QTLs (eQTLs) located on most of the 21 wheat chromosomes were detected for the studied traits. Of which, a total of seven stable QTLs and three major QTLs were detected. In addition, an InDel marker closely linked to the stable major QTL,
qShl-3B
was developed and validated in 188 RILs, providing important information for the genetic improvement and development of salt and drought tolerance wheat varieties.
Journal Article