Using UAV-Based Temporal Spectral Indices to Dissect Changes in the Stay-Green Trait in Wheat

Stay-green (SG) in wheat is a beneficial trait that increases yield and stress tolerance. However, conventional phenotyping techniques limited the understanding of its genetic basis. Spectral indices (SIs) as non-destructive tools to evaluate crop temporal senescence provide an alternative strategy. Here, we applied SIs to monitor the senescence dynamics of 565 diverse wheat accessions from anthesis to maturation stages over 2 field seasons. Four SIs (normalized difference vegetation index, green normalized difference vegetation index, normalized difference red edge index, and optimized soil-adjusted vegetation index) were normalized to develop relative stay-green scores (RSGS) as the SG indicators. An RSGS-based genome-wide association study identified 47 high-confidence quantitative trait loci (QTL) harboring 3,079 single-nucleotide polymorphisms associated with SG and 1,085 corresponding candidate genes. Among them, 15 QTL overlapped or were adjacent to known SG-related QTL/genes, while the remaining QTL were novel. Notably, a set of favorable haplotypes of SG-related candidate genes such as TraesCS2A03G1081100, TracesCS6B03G0356400, and TracesCS2B03G1299500 are increasing following the Green Revolution, further validating the feasibility of the pipeline. This study provided a valuable reference for further quantitative SG and genetic research in diverse wheat panels.

Evaluation of force pain thresholds to ensure collision safety in worker-robot collaborative operations

With the growing demand for robots in the industrial field, robot-related technologies with various functions have been introduced. One notable development is the implementation of robots that operate in collaboration with human workers to share tasks, without the need of any physical barriers such as safety fences. The realization of such collaborative operations in practice necessitates the assurance of safety if humans and robots collide. Thus, it is important to establish criteria for such collision scenarios to ensure robot safety and prevent injuries. Collision safety must be ensured in both pinching (quasi-static contact) and impact (transient contact) situations. To this end, we measured the force pain thresholds associated with impacts and evaluated the biomechanical limitations. This measurements were obtained through clinical trials involving physical collisions between human subjects and a device designed for generating impacts, and the force pain thresholds associated with transient collisions between humans and robots were analyzed. Specifically, the force pain threshold was measured at two different locations on the bodies of 37 adults aged 19-32 years, using two impactors with different shapes. The force pain threshold was compared with the results of other relevant studies. The results can help identify biomechanical limitations in a precise and reliable manner to ensure the safety of robots in collaborative applications.

Genome-wide QTL mapping for agronomic traits in the winter wheat cultivar Pindong 34 based on 90K SNP array

Introduction

Agronomic traits are key components of wheat yield. Exploitation of the major underlying quantitative trait loci (QTLs) can improve the yield potential in wheat breeding.

Methods

In this study, we constructed a recombinant inbred line (RIL) population from Mingxian 169 (MX169) and Pindong 34 (PD34) to determine the QTLs for grain length (GL), grain width (GW), grain length-to-width ratio (LWR), plant height (PH), spike length (SL), grain number per spike (GNS), and the thousand grain weight (TGW) across four environments using wheat 90K SNP array.

Results

A QTL associated with TGW, i.e., QTGWpd.swust-6BS, was identified on chromosome 6B, which explained approximately 14.1%-16.2% of the phenotypic variation. In addition, eight QTLs associated with GL were detected across six chromosomes in four different test environments. These were QGLpd.swust-1BL, QGLpd.swust-2BL, QGLpd.swust-3BL.1, QGLpd.swust-3BL.2, QGLpd.swust-5DL, QGLpd.swust-6AL, QGLpd.swust-6DL.1, and QGLpd.swust-6DL.2. They accounted for 9.0%-21.3% of the phenotypic variation. Two QTLs, namely, QGWpd.swust-3BS and QGWpd.swust-6DL, were detected for GW on chromosomes 3B and 6D, respectively. These QTLs explained 12.8%-14.6% and 10.8%-15.2% of the phenotypic variation, respectively. In addition, two QTLs, i.e., QLWRpd.swust-7AS.1 and QLWRpd.swust-7AS.2, were detected on chromosome 7A for the grain LWR, which explained 10.9%-11.6% and 11.6%-11.2% of the phenotypic variation, respectively. Another QTL, named QGNSpd-swust-6DS, was discovered on chromosome 6D, which determines the GNS and which accounted for 11.4%-13.8% of the phenotypic variation. Furthermore, five QTLs associated with PH were mapped on chromosomes 2D, 3A, 5A, 6B, and 7B. These QTLs were QPHpd.swust-2DL, QPHpd.swust-3AL, QPHpd.swust-5AL, QPHpd.swust-6BL, and QPHpd.swust-7BS, which accounted for 11.3%-19.3% of the phenotypic variation. Lastly, a QTL named QSLpd.swust-3AL, conferring SL, was detected on chromosome 3A and explained 16.1%-17.6% of the phenotypic variation. All of these QTLs were defined within the physical interval of the Chinese spring reference genome.

Discussion

The findings of this study have significant implications for the development of fine genetic maps, for genomic breeding, and for marker-assisted selection to enhance wheat grain yield.

The value of T2-weighted MRI contrast ratio combined with DWI in evaluating the pathological grade of solid lung adenocarcinoma

AIM

To assess the predictive value of T2-weighted (T2W) magnetic resonance imaging (MRI) in combination with diffusion-weighted imaging (DWI) for determining the pathological grading of solid lung adenocarcinoma.

MATERIALS AND METHODS

The clinical and imaging data from 153 cases of solid lung adenocarcinoma (82 men, 71 women, mean age 63.2 years) confirmed at histopathology in The First Affiliated Hospital of Xi'an Jiaotong University from January 2017 to May 2022 were analysed retrospectively. Adenocarcinomas were classified into low-grade (G1 and G2) and high-grade (G3) groups following the 2020 pathological grading system proposed by the International Association for the Study of Lung Cancer. The T2-weighted contrast ratio (T2CR), calculated as the T2 signal intensity of the lung mass/nodule divided by the T2 signal intensity of the right rhomboid muscle was utilised. Two experienced radiologists reviewed the MRI images independently, measured the T2CR, and obtained apparent diffusion coefficient (ADC) values. The Mann-Whitney U-test was used to compare general characteristics (sex, age, maximum diameter), T2CR, and ADC values between the low-grade and high-grade groups. The non-parametric Kruskal-Wallis test determined differences in T2CR and ADC values among the five adenocarcinoma subtypes. Receiver characteristic curve (ROC) analysis, along with area under the curve (AUC) calculation, assessed the effectiveness of each parameter in distinguishing the pathological grade of lung adenocarcinoma. A Z-test was used to compare the AUC values.

RESULTS

Among the 153 patients with adenocarcinoma, 103 had low-grade adenocarcinoma, and 50 had high-grade adenocarcinoma. The agreement between T2CR and ADC observers was good (0.948 and 0.929, respectively). None of the parameters followed a normal distribution (p<0.05). The ADC value was lower in the high-grade adenocarcinoma group compared to the low-grade adenocarcinoma group (p=0.004), while the T2CR value was higher in the high-grade group (p=0.011). Statistically significant differences were observed in maximum diameter and gender between the two groups (p<0.001 and p=0.005, respectively), while no significant differences were noted in age (p=0.980). Among the five adenocarcinoma subtypes, only the lepidic and micropapillary subtypes displayed statistical differences in ADC values (p=0.047), with the remaining subtypes showing no statistical differences (p>0.05). The AUC values for distinguishing high-grade adenocarcinoma from low-grade adenocarcinoma were 0.645 for ADC and 0.627 for T2CR. Combining T2CR, ADC, sex, and maximum diameter resulted in an AUC of 0.778, sensitivity of 70%, and specificity of 75%. This combination significantly improved diagnostic efficiency compared to T2CR and ADC alone (p=0.008, z = 2.624; p=0.007, z = 2.679).

CONCLUSION

The MRI quantitative parameters are useful for distinguishing the pathological grades of solid lung adenocarcinoma, offering valuable insights for precise lung cancer treatment.

Host genotype-specific rhizosphere fungus enhances drought resistance in wheat

BACKGROUND

The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses.

RESULTS

Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum).

CONCLUSIONS

Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.

Genetic dissection and identification of stripe rust resistance genes in the wheat cultivar Lanhangxuan 121, a cultivar selected from a space mutation population

Stripe rust is a devastating disease of wheat worldwide. Chinese wheat cultivar Lanhangxuan 121 (LHX121), selected from an advanced line L92-47 population that had been subjected to space mutation breeding displayed a consistently higher level of resistance to stipe rust than its parent in multiple field environments. The aim of this research was to establish the number and types of resistance genes in parental lines L92-47 and LHX121 using separate segregating populations. The first population developed from a cross between LHX121 and susceptible cultivar Xinong 822 comprised 278 F2:3 lines. The second validation population comprised 301 F2:3 lines from a cross between L92-47 and susceptible cultivar Xinong 979. Lines of two population were evaluated for stripe rust response at three sites during the 2018-2020 cropping season. Affymetrix 660 K SNP arrays were used to genotype the lines and parents. Inclusive composite interval mapping detected QTL QYrLHX.nwafu-2BS, QYrLHX.nwafu-3BS, and QYrLHX.nwafu-5BS for resistance in all three environments. Based on previous studies and pedigree information, QYrLHX.nwafu-2BS and QYrLHX.nwafu-3BS were likely to be Yr27 and Yr30 that are present in the L92-47 parent. QYrLHX.nwafu-5BS (YrL121) detected only in LHX121 was mapped to a 7.60 cM interval and explained 10.67-22.57% of the phenotypic variation. Compared to stripe rust resistance genes previously mapped to chromosome 5B, YrL121 might be a new adult plant resistance QTL. Furthermore, there were a number of variations signals using 35 K SNP array and differentially expressed genes using RNA-seq between L92-47 and LHX121 in the YrL121 region, indicating that they probably impair the presence and/or function of YrL121.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01461-0.

Seed-to-Seed: Plant Core Vertically Transmitted Microbiota

The plant core microbiota transmitted by seeds have been demonstrated to exist in seeds and adult plants of several crops for multiple generations. They are closely related to plants and are relatively conserved throughout evolution, domestication, and breeding. These microbiota play a vital role in the early stages of plant growth. However, information about their colonization routes, transmission pathways, and final fate remains fragmentary. This review delves into the concept of these microbiota, their colonization sources, transmission pathways, and how they change throughout plant evolution, domestication, and breeding, as well as their effects on plants, based on relevant literature. Finally, the significant potential of incorporating the practical application of seed-transmitted microbiota into plant microbial breeding is emphasized.

[Expert consensus on the biobank development of oral genetic diseases and rare diseases and storage codes of related biological samples from craniofacial and oral region]

The biological samples of oral genetic diseases and rare diseases are extremely precious. Collecting and preserving these biological samples are helpful to elucidate the mechanisms and improve the level of diagnose and treatment of oral genetic diseases and rare diseases. The standardized construction of biobanks for oral genetic diseases and rare diseases is important for achieving these goals. At present, there is very little information on the construction of these biobanks, and the standards or suggestions for the classification and coding of biological samples from oral and maxillofacial sources, and this is not conducive to the standardization and information construction of biobanks for special oral diseases. This consensus summarizes the background, necessity, principles, and key points of constructing the biobank for oral genetic diseases and rare diseases. On the base of the group standard "Classification and Coding for Human Biomaterial" (GB/T 39768-2021) issued by the National Technical Committee for Standardization of Biological Samples, we suggest 76 new coding numbers for different of biological samples from oral and maxillofacial sources. We hope the consensus may promote the standardization, and smartization on the biobank construction as well as the overall research level of oral genetic diseases and rare diseases in China.

[Measurement and analysis of the crown conical degree of maxillary incisors in patients with congenital tooth agenesis caused by different gene mutations]

Objective: To measure the crown conical degree of the remaining maxillary incisors in patients with congenital tooth agenesis, and to analyze the influence of different gene mutations on the crown conical degree of patients. Methods: Whole exome sequencing was performed on 85 patients with congenital tooth agenesis (50 males, 35 females, median age 19 years old) who visited the Department of Prosthodontics, Peking University School and Hospital of Stomatology from January 2019 to January 2023. The pathogenic gene was identified. The width of the crowns of the maxillary central and lateral incisors at the incisal 1/3 and gingival 1/3 were measured on the panoramic radiograph, and the ratio was defined as the crown conical degree. The smaller the ratio is, the more likely is the crown to be peg shaped teeth. The control group was matched by age and gender with 85 other patients with intact maxillary permanent incisors who were treated in the Department of Prosthodontics, Peking University School and Hospital of Stomatology from January 2019 to January 2023. The conical degree of the tooth agenesis group was compared with the control group by t-test, and the differences in the crown conical degree in different gene mutation groups were compared using one-way analysis of variance, and the multiple comparisons among gene groups were carried out using the LSD method. Results: Among the 85 tooth agenesis patients, the numbers of patients in each gene mutation group were 20 in ectodysplasin A (EDA) group, 8 in ectodysplasin A receptor (EDAR) group, 15 in wingless-type MMTV integration site family, member 10A (WNT10A) group, 16 in paired box 9 (PAX9) group, 10 in Msh homeobox 1 (MSX1) group, 10 in low-density lipoprotein receptor related protein 6 (LRP6) group, and 6 in bone morphogenetic protein4 (BMP4) group. The number of missing teeth were 1-27, median number 15 among the tooth agenesis patients. There was no significant difference in the conical degree between the left and right homonymous teeth in the congenital tooth agenesis group and the control group (P>0.05). The crown conical degree of maxillary central incisor and lateral incisor in the congenital missing teeth group (0.95±0.24, 0.90±0.22) was significantly smaller than that in the control group (1.12±0.09, 1.13±0.09) (t=-8.50, P<0.001; t=-11.47, P<0.001). In WNT10A mutants, the conical degree of lateral incisors (0.89±0.18) was less than that of central incisors (1.07±0.15)(t=3.68, P<0.001). The conical degree of central incisors and lateral incisors (0.70±0.23, 0.57±0.15) of EDA mutants was significantly lower than that in patients with other gene mutations (P>0.05). Conclusions: Compared with the normal control group, the remaining maxillary central and lateral incisors of the seven gene mutation groups of patients with congenital tooth agenesis all had different degrees of conical crown. Among them, the crown conical degree of maxillary central and lateral incisors of the EDA mutation was the most severe, and the WNT10A mutation affected the maxillary lateral incisors more specifically.

Slow stripe rusting in Chinese wheat Jimai 44 conferred by Yr29 in combination with a major QTL on chromosome arm 6AL

YrJ44, a more effective slow rusting gene than Yr29, was localized to a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479 on chromosome 6AL. "Slow rusting" (SR) is a type of adult plant resistance (APR) that can provide non-specific durable resistance to stripe rust in wheat. Chinese elite wheat cultivar Jimai 44 (JM44) has maintained SR to stripe rust in China since its release despite exposure to a changing and variable pathogen population. An F2:6 population comprising 295 recombinant inbred lines (RILs) derived from a cross between JM44 and susceptible cultivar Jimai 229 (JM229) was used in genetic analysis of the SR. The RILs and parental lines were evaluated for stripe rust response in five field environments and genotyped using the Affymetrix Wheat55K SNP array and 13 allele-specific quantitative PCR-based (AQP) markers. Two stable QTL on chromosome arms 1BL and 6AL were identified by inclusive composite interval mapping. The 1BL QTL was probably the pleiotropic gene Lr46/Yr29/Sr58. QYr.nwafu-6AL (hereafter named YrJ44), mapped in a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479, was more effective than Yr29 in reducing disease severity and relative area under the disease progress curve (rAUDPC). RILs harboring both YrJ44 and Yr29 displayed levels of SR equal to the resistant parent JM44. The AQP markers linked with YrJ44 were polymorphic and significantly correlated with stripe rust resistance in a panel of 1,019 wheat cultivars and breeding lines. These results suggested that adequate SR resistance can be obtained by combining YrJ44 and Yr29 and the AQP markers can be used in breeding for durable stripe rust resistance.

Identification of Long Intergenic Noncoding RNAs in Rhizoctonia cerealis following Inoculation of Wheat

Wheat sharp eyespot caused by Rhizoctonia cerealis is primarily a severe threat to worldwide wheat production. Currently, there are no resistant wheat cultivars, and the use of fungicides is the primary method for controlling this disease. Elucidating the mechanisms of R. cerealis pathogenicity can accelerate the pace of the control of this disease. Long intergenic noncoding RNAs (lincRNAs) that function in plant-pathogen interactions might provide a new perspective. We systematically analyzed lincRNAs and identified a total of 1,319 lincRNAs in R. cerealis. We found that lincRNAs are involved in various biological processes, as shown by differential expression analysis and weighted correlation network analysis (WGCNA). Next, one of nine hub lincRNAs in the blue module that was related to infection and growth processes, MSTRG.4380.1, was verified to reduce R. cerealis virulence on wheat by a host-induced gene silencing (HIGS) assay. Following that, RNA sequencing (RNA-Seq) analysis revealed that the significantly downregulated genes in the MSTRG.4380.1 knockdown lines were associated mainly with infection-related processes, including hydrolase, transmembrane transporter, and energy metabolism activities. Additionally, 23 novel microRNAs (miRNAs) were discovered during small RNA (sRNA) sequencing (sRNA-Seq) analysis of MSTRG.4380.1 knockdown, and target prediction of miRNAs suggested that MSTRG.4380.1 does not act as a competitive endogenous RNA (ceRNA). This study performed the first genome-wide identification of R. cerealis lincRNAs and miRNAs. It confirmed the involvement of a lincRNA in the infection process, providing new insights into the mechanism of R. cerealis infection and offering a new approach for protecting wheat from R. cerealis. IMPORTANCE Rhizoctonia cerealis, the primary causal agent of wheat sharp eyespot, has caused significant losses in worldwide wheat production. Since no resistant wheat cultivars exist, chemical control is the primary method. However, this approach is environmentally unfriendly and costly. RNA interference (RNAi)-mediated pathogenicity gene silencing has been proven to reduce the growth of Rhizoctonia and provides a new perspective for disease control. Recent studies have shown that lincRNAs are involved in various biological processes across species, such as biotic and abiotic stresses. Therefore, verifying the function of lincRNAs in R. cerealis is beneficial for understanding the infection mechanism. In this study, we reveal that lincRNAs could contribute to the virulence of R. cerealis, which provides new insights into controlling this pathogen.

Molecular characterization and validation of adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895

KEY MESSAGE

Adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895 was mapped to the physical interval 710.2-713.2 Mb on the long arm of chromosome 2A. Adult-plant resistance to stripe rust is generally more durable than all-stage resistance. Chinese wheat cultivar Zhongmai 895 showed stable stripe rust resistance at the adult-plant stage. To map the genetic loci underlying its resistance, 171 doubled haploid (DH) lines from a Yangmai 16/Zhongmai 895 cross were genotyped with the wheat 660 K SNP chip. Disease severities of the DH population and parents were assessed in four environments. A major QTL designated QYryz.caas-2AL was mapped to interval 703.7-715.3 Mb on the long arm of chromosome 2A using both chip-based and KASP (kompetitive allele-specific PCR) marker-based methods, explaining 31.5 to 54.1% of the phenotypic variances. The QTL was further validated in an F₂ population of cross Emai 580/Zhongmai 895 with 459 plants and a panel of 240 wheat cultivars using KASP markers. Three reliable KASP markers predicted a low frequency (7.2-10.5%) of QYryz.caas-2AL in the test panel and remapped the gene to the physical interval 710.2-713.2 Mb. Based on different physical positions or genetic effects from known genes or QTL on chromosome arm 2AL, the gene was predicted to be a new one for adult-plant stripe rust resistance and was named Yr86. Twenty KASP markers linked to Yr86 were developed in this study based on wheat 660 K SNP array and genome re-sequencing. Three of them are significantly associated with stripe rust resistance in natural population. These markers should be useful for marker-assisted selection and also provide a starting point for fine mapping and map-based cloning of the new resistance gene.

Genome-wide association study reveals the genetic variation and candidate gene for grain calcium content in bread wheat

KEY MESSAGE

This study provides important information on the genetic basis of GCaC in wheat, thus contributing to breeding efforts to improve the nutrient quality of wheat. Calcium (Ca) plays important roles in the human body. Wheat grain provides the main diet for billions of people worldwide but is low in Ca content. Here, grain Ca content (GCaC) of 471 wheat accessions was determined in four field environments. A genome-wide association study (GWAS) was performed to reveal the genetic basis of GCaC using the phenotypic data form four environments and a wheat 660 K single nucleotide polymorphism (SNP) array. Twelve quantitative trait locus (QTLs) for GCaC were identified on chromosomes 1A, 1D, 2A, 3B, 6A, 6D, 7A, and 7D, which was significant in at least two environments. Haplotype analysis revealed that the phenotypic difference between the haplotypes of TraesCS6D01G399100 was significant (P ≤ 0.05) across four environments, suggesting it as an important candidate gene for GCaC. This research enhances our understanding of the genetic architecture of GCaC for further improving the nutrient quality of wheat.

[Development and validation of prognostic nomogram for malignant pleural mesothelioma]

Objective: To development the prognostic nomogram for malignant pleural mesothelioma (MPM). Methods: Two hundred and ten patients pathologically confirmed as MPM were enrolled in this retrospective study from 2007 to 2020 in the People's Hospital of Chuxiong Yi Autonomous Prefecture, the First and Third Affiliated Hospital of Kunming Medical University, and divided into training (n=112) and test (n=98) sets according to the admission time. The observation factors included demography, symptoms, history, clinical score and stage, blood cell and biochemistry, tumor markers, pathology and treatment. The Cox proportional risk model was used to analyze the prognostic factors of 112 patients in the training set. According to the results of multivariate Cox regression analysis, the prognostic prediction nomogram was established. C-Index and calibration curve were used to evaluate the model's discrimination and consistency in raining and test sets, respectively. Patients were stratified according to the median risk score of nomogram in the training set. Log rank test was performed to compare the survival differences between the high and low risk groups in the two sets. Results: The median overall survival (OS) of 210 MPM patients was 384 days (IQR=472 days), and the 6-month, 1-year, 2-year, and 3-year survival rates were 75.7%, 52.6%, 19.7%, and 13.0%, respectively. Cox multivariate regression analysis showed that residence (HR=2.127, 95% CI: 1.154-3.920), serum albumin (HR=1.583, 95% CI: 1.017-2.464), clinical stage (stage Ⅳ: HR=3.073, 95% CI: 1.366-6.910) and the chemotherapy (HR=0.476, 95% CI: 0.292-0.777) were independent prognostic factors for MPM patients. The C-index of the nomogram established based on the results of Cox multivariate regression analysis in the training and test sets were 0.662 and 0.613, respectively. Calibration curves for both the training and test sets showed moderate consistency between the predicted and actual survival probabilities of MPM patients at 6 months, 1 year, and 2 years. The low-risk group had better outcomes than the high-risk group in both training (P=0.001) and test (P=0.003) sets. Conclusion: The survival prediction nomogram established based on routine clinical indicators of MPM patients provides a reliable tool for prognostic prediction and risk stratification.

Performance of Active-Quenching SPAD Array Based on the Tri-State Gates of FPGA and Packaged with Bare Chip Stacking

The performance of an active-quenching single-photon avalanche diode (SPAD) array that is based on the tri-state gates of a field programmable gate array (FPGA) is presented. The array is implemented by stacking a bare 4 × 4 N-on-P SPAD array on a bare FPGA die, and the electrodes of the SPAD pixels and the I/O ports of the FPGA are connected through wire bonding within the same package. The active quenching action on each SPAD pixel is performed by using the properties of the tri-state gates of the FPGA. Digital signal processing, such as pulse counters, data encoders, and command interactions, is also performed by using the same FPGA. The breakdown voltage of the SPAD pixels, with an active area of 60 μm × 60 μm, is 47.2-48.0 V. When the device is reverse biased at a voltage of ~50.4 V, a response delay of ~50 ns, a dead time of 157 ns, a dark count rate of 2.44 kHz, and an afterpulsing probability of 6.9% are obtained. Its peak photon detection probability (PDP) reaches 17.0% at a peak wavelength of 760 nm and remains above 10% at 900 nm. This hybrid integrated SPAD array is reconfigurable and cost effective.

Core root-associated prokaryotic community and its relationship to host traits across wheat varieties

The root-associated microbiomes play important roles in plant growth. However, it is largely unknown how wheat variety evolutionary relatedness shapes each subcommunity in the root microbiome and, in turn, how these microbes affect wheat yield and quality. Here we studied the prokaryotic communities associated with the rhizosphere and root endosphere in 95 wheat varieties at regreening and heading stages. The results indicated that the less diverse but abundant core prokaryotic taxa occurred among all varieties. Among these core taxa, we identified 49 and 108 heritable amplicon sequence variants, whose variations in relative abundances across the root endosphere and rhizosphere samples were significantly affected by wheat variety. The significant correlations between phylogenetic distance of wheat varieties and prokaryotic community dissimilarity were only observed in non-core and abundant subcommunities in the endosphere samples. Again, wheat yield was only significantly associated with root endosphere microbiota at the heading stage. Additionally, wheat yield could be predicted using the total abundance of 94 prokaryotic taxa as an indicator. Our results demonstrated that the prokaryotic communities in the root endosphere had higher correlations with wheat yield and quality than those in the rhizosphere; thus, managing root endosphere microbiota, especially core taxa, through agronomic practices and crop breeding, is important for promoting wheat yield and quality.

High density mapping of wheat stripe rust resistance gene QYrXN3517-1BL using QTL mapping, BSE-Seq and candidate gene analysis

Fine mapping of a major stripe rust resistance locus QYrXN3517-1BL to a 336 kb region that includes 12 candidate genes. Utilization of genetic resistance is an effective strategy to control stripe rust disease in wheat. Cultivar XINONG-3517 (XN3517) has remained highly resistant to stripe rust since its release in 2008. To understand the genetic architecture of stripe rust resistance, Avocet S (AvS) × XN3517 F₆ RIL population was assessed for stripe rust severity in five field environments. The parents and RILs were genotyped by using the GenoBaits Wheat 16 K Panel. Four stable QTL from XINONG-3517 were detected on chromosome arms 1BL, 2AL, 2BL, and 6BS, named as QYrXN3517-1BL, QYrXN3517-2AL, QYrXN3517-2BL, and QYrXN3517-6BS, respectively. Based on the Wheat 660 K array and bulked segregant exome sequencing (BSE-Seq), the most effective QTL on chromosome 1BL is most likely different from the known adult plant resistance gene Yr29 and was mapped to a 1.7 cM region [336 kb, including twelve candidate genes in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0]. The 6BS QTL was identified as Yr78, and the 2AL QTL was probably same as QYr.caas-2AL or QYrqin.nwafu-2AL. The novel QTL on 2BL was effective in seedling stage against the races used in phenotyping. In addition, allele-specifc quantitative PCR (AQP) marker nwafu.a5 was developed for QYrXN3517-1BL to assist marker-assisted breeding.

Allelic variation of TaWD40-4B.1 contributes to drought tolerance by modulating catalase activity in wheat

Drought drastically restricts wheat production, so to dissect allelic variations of drought tolerant genes without imposing trade-offs between tolerance and yield is essential to cope with the circumstance. Here, we identify a drought tolerant WD40 protein encoding gene TaWD40-4B.1 of wheat via the genome-wide association study. The full-length allele TaWD40-4B.1^C but not the truncated allele TaWD40-4B.1^T possessing a nonsense nucleotide variation enhances drought tolerance and grain yield of wheat under drought. TaWD40-4B.1^C interacts with canonical catalases, promotes their oligomerization and activities, and reduces H₂O₂ levels under drought. The knock-down of catalase genes erases the role of TaWD40-4B.1^C in drought tolerance. TaWD40-4B.1^C proportion in wheat accessions is negatively correlative with the annual rainfall, suggesting this allele may be selected during wheat breeding. The introgression of TaWD40-4B.1^C enhances drought tolerance of the cultivar harboring TaWD40-4B.1^T. Therefore, TaWD40-4B.1^C could be useful for molecular breeding of drought tolerant wheat.

Development of breeder chip for gene detection and molecular-assisted selection by target sequencing in wheat

Wheat is an essential food crop and its high and stable yield is suffering from great challenges due to the limitations of current breeding technology and various stresses. Accelerating molecularly assisted stress-resistance breeding is critical. Through a meta-analysis of published loci in wheat over the last two decades, we selected 60 loci with main breeding objectives, high heritability, and reliable genotyping, such as stress resistance, yield, plant height, and resistance to spike germination. Then, using genotyping by target sequencing (GBTS) technology, we developed a liquid phase chip based on 101 functional or closely linked markers. The genotyping of 42 loci was confirmed in an extensive collection of Chinese wheat cultivars, indicating that the chip can be used in molecular-assisted selection (MAS) for target breeding goals. Besides, we can perform the preliminary parentage analysis with the genotype data. The most significant contribution of this work lies in translating a large number of molecular markers into a viable chip and providing reliable genotypes. Breeders can quickly screen germplasm resources, parental breeding materials, and intermediate materials for the presence of excellent allelic variants using the genotyping data by this chip, which is high throughput, convenient, reliable, and cost-efficient.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01359-3.

Genome-wide association study for grain zinc concentration in bread wheat (Triticum aestivum L.)

Introduction

Zinc (Zn) deficiency causes serious diseases in people who rely on cereals as their main food source. However, the grain zinc concentration (GZnC) in wheat is low. Biofortification is a sustainable strategy for reducing human Zn deficiency.

Methods

In this study, we constructed a population of 382 wheat accessions and determined their GZnC in three field environments. Phenotype data was used for a genome-wide association study (GWAS) using a 660K single nucleotide polymorphism (SNP) array, and haplotype analysis identified an important candidate gene for GZnC.

Results

We found that GZnC of the wheat accessions showed an increasing trend with their released years, indicating that the dominant allele of GZnC was not lost during the breeding process. Nine stable quantitative trait loci (QTLs) for GZnC were identified on chromosomes 3A, 4A, 5B, 6D, and 7A. And an important candidate gene for GZnC, namely, TraesCS6D01G234600, and GZnC between the haplotypes of this gene showed, significant difference (P ≤ 0.05) in three environments.

Discussion

A novel QTL was first identified on chromosome 6D, this finding enriches our understanding of the genetic basis of GZnC in wheat. This study provides new insights into valuable markers and candidate genes for wheat biofortification to improve GZnC.

[Sero-epidemiological characteristics of the hepatitis D virus infection among hepatitis B virus infected-patients at a single center in Xinjiang region]

Objective: To investigate the sero-epidemiological characteristics of the hepatitis D virus (HDV) infection among hepatitis B virus (HBV)-infected patients in Xinjiang region. Methods: A single-center cross-sectional analysis method was used to select 264 cases of hepatitis B virus infection who were hospitalized in the Center for Infectious Diseases and Liver Diseases of the First Affiliated Hospital of Xinjiang Medical University from August 2021 to January 2022. All patients were tested for HDV Ag, HDV IgM, HDV IgG, and HDV RNA. The infection status of hepatitis D virus was analyzed by grouping according to their clinical type, HBV viral load, and HBsAg level. A paired t-test was used for data with measurement data conforming to normal distribution. A paired rank sum test was used for data that did not conform to normal distribution before and after treatment. Results: A total of 36 cases (13.64%) and 26 cases (9.85%) were positive for HDV serological markers and HDV RNA. According to clinical type grouping, the positive rates of HDV serum markers in patients with chronic hepatitis B, hepatitis B-related cirrhosis, liver cancer, and liver failure were 13.46%, 12.43%, and 20.83%, respectively, and there was no statistically significant difference among the three groups (χ²=0.86, P=0.649). The positive rates of HDV RNA were 11.54%, 8.11%, and 20.83%, respectively, and there was no statistically significant difference among the three groups (χ²=4.015, P=0.134). According to HBV viral load grouping, the positive rates of HDV serum markers among patients with viral loads <20, 20-2 000, and >2 000 IU/ml were 17.15%, 7.81%, and 6.67%, respectively, and the difference was not statistically significant among the three groups (χ²=4.846, P=0.089). The positive rates of HDV RNA were 9.47%, 10.94%, and 10%, respectively, and the difference was not statistically significant among the three groups (χ²=0.113, P=0.945). According to HBsAg level grouping, the positive rates of HDV serum markers in HBsAg<0.05, 0.05~250, and >250 IU/ml were 14.29%, 16.67%, and 10.85%, respectively, and there was no statistically significance between the three groups (χ²=1.745, P=0.418). The positive rates of HDV RNA were 4.76%, 8.77%, and 11.63%, respectively, and there was no statistically significant difference among the three groups (χ²=1.221, P=0.543). Clinical outcome, disease course, HBV DNA, serological markers of viral hepatitis, routine blood test, biochemical indicators, coagulation function, and other laboratory indicators were compared between HDV serum marker and/or nucleic acid positive and negative patients, and there was no statistically significant difference (P>0.05). Conclusion: The positive rate of HDV serological markers and HDV RNA is 13.64% and 9.85%, respectively, at a single center in the Xinjiang region, and there is still a high HDV infection rate among the HBV-infected patients with low levels of viral load and HBsAg.

Reduction of Rhizoctonia cerealis Infection on Wheat Through Host- and Spray-Induced Gene Silencing of an Orphan Secreted Gene

Rhizoctonia cerealis is a soilborne fungus that can cause sharp eyespot in wheat, resulting in massive yield losses found in many countries. Due to the lack of resistant cultivars, fungicides have been widely used to control this pathogen. However, chemical control is not environmentally friendly and is costly. Meanwhile, the lack of genetic transformation tools has hindered the functional characterization of virulence genes. In this study, we attempted to characterize the function of virulence genes by two transient methods, host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS), which use RNA interference to suppress the pathogenic development. We identified ten secretory orphan genes from the genome. After silencing these ten genes, only the RcOSP1 knocked-down plant significantly inhibited the growth of R. cerealis. We then described RcOSP1 as an effector that could impair wheat biological processes and suppress pathogen-associated molecular pattern-triggered immunity in the infection process. These findings confirm that HIGS and SIGS can be practical tools for researching R. cerealis virulence genes. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

MRI-based radiomics analysis in differentiating solid non-small-cell from small-cell lung carcinoma: a pilot study

AIM

To investigate the ability of a T2-weighted (W) magnetic resonance imaging (MRI)-based radiomics signature to differentiate solid non-small-cell lung carcinoma (NSCLC) from small-cell lung carcinoma (SCLC).

MATERIALS AND METHODS

The present retrospective study enrolled 152 eligible patients (NSCLC = 125, SCLC = 27). All patients underwent MRI using a 3 T scanner and radiomics features were extracted from T2W MRI. The least absolute shrinkage and selection operator (LASSO) logistic regression model was used to identify the optimal radiomics features for the construction of a radiomics model to differentiate solid NSCLC from SCLC. Threefold cross validation repeated 10 times was used for model training and evaluation. The conventional MRI morphology features of the lesions were also evaluated. The performance of the conventional MRI morphological features, and the radiomics signature model and nomogram model (combining radiomics signature with conventional MRI morphological features) was evaluated using receiver operating characteristic (ROC) curve analysis.

RESULTS

Five optimal features were chosen to build a radiomics signature. There was no significant difference in age, gender, and the largest diameter. The radiomics signature and conventional MRI morphological features (only pleural indentation and lymph node enlargement) were independent predictive factors for differentiating solid NSCLC from SCLC. The area under the ROC curves (AUCs) for MRI morphological features, and the radiomics model, and nomogram model was 0.69, 0.85, and 0.90 (ROC), respectively.

CONCLUSIONS

The T2W MRI-based radiomics signature is a potential non-invasive approach for distinguishing solid NSCLC from SCLC.

Genome-Wide QTL Mapping for Stripe Rust Resistance in Winter Wheat Pindong 34 Using a 90K SNP Array

Winter wheat cultivar Pindong 34 has both adult-plant resistance (APR) and all-stage resistance (ASR) to stripe rust, which is caused by Puccinia striiformis f. sp. tritici (Pst). To map the quantitative trait loci (QTL) for stripe rust resistance, an F_6-10 recombinant inbred line (RIL) population from a cross of Mingxian 169 × Pingdong 34 was phenotyped for stripe rust response over multiple years in fields under natural infection conditions and with selected Pst races under controlled greenhouse conditions, and genotyping was performed with a 90K single nucleotide polymorphism (SNP) array chip. Inclusive composite interval mapping (ICIM) identified 12 APR resistance QTLs and 3 ASR resistance QTLs. Among the 12 APR resistance QTLs, QYrpd.swust-1BL (explaining 9.24-13.33% of the phenotypic variation), QYrpd.swust-3AL.1 (11.41-14.80%), QYrpd.swust-3AL.2 (11.55-16.10%), QYrpd.swust-6BL (9.39-12.78%), QYrpd.swust-6DL (9.52-16.36%), QYrpd.swust-7AL (9.09-17.0%), and QYrpd.swust-7DL (8.87-11.38%) were more abundant than in the five tested environments and QYrpd.swust-1AS (11.05-12.72%), QYrpd.swust-1DL (9.81-13.05%), QYrpd.swust-2BL.1 (9.69-10.57%), QYrpd.swust-2BL.2 (10.36-12.97%), and QYrpd.swust-2BL.3 (9.54-13.15%) were significant in some of the tests. The three ASR resistance QTLs QYrpd.swust-2AS (9.69-13.58%), QYrpd.swust-2BL.4 (9.49-12.07%), and QYrpd.swust-7AS (16.16%) were detected based on the reactions in the seedlings tested with the CYR34 Pst race. Among the 15 QTLs detected in Pindong 34, the ASR resistance gene QYrpd.swust-7AS mapped on the short arm of chromosome 7A was likely similar to the previously reported QTL Yr61 in the region. The QTLs identified in the present study and their closely linked molecular markers could be useful for developing wheat cultivars with durable resistance to stripe rust.

Epistatic interaction effect between chromosome 1BL (Yr29) and a novel locus on 2AL facilitating resistance to stripe rust in Chinese wheat Changwu 357-9

Four stable QTL for adult plant resistance were identified in wheat line Changwu 357-9, including a new QTL on 2AL showing significant interaction with Yr29 to reduce stripe rust severity. Stripe rust (yellow rust) is a serious disease of bread wheat (Triticum aestivum L.) worldwide. Genetic resistance is considered the most economical, effective and environmentally friendly method to control the disease and to minimize the use of fungicides. The current study focused on characterizing the components of stripe rust resistance and understanding the interactions in Changwu 357-9 (CW357-9)/Avocet S RIL population. A genetic linkage map constructed using a new GenoBaits Wheat 16K Panel and the 660K SNP array had 5104 polymorphic SNP markers spanning 3533.11 cM. Four stable QTL, consistently identified across five environments, were detected on chromosome arms 1BL, 2AL, 3DS, and 6BS in Changwu357-9. The most effective QTL QYrCW357-1BL was Yr29. The 6BS QTL was identified as Yr78, which has been combined with the 1BL QTL in many wheat cultivars and breeding lines. The novel QTL on 2AL with moderate effect showed a stable and significant epistatic interaction with Yr29. The QTL on 3DL should be same as QYrsn.nwafu-3DL and enriches the overall stripe rust resistance gene pool for breeding. Polymorphisms of flanking AQP markers AX-110020417 (for QYrCW357-1BL), AX-110974948 (for QYrCW357-2AL), AX-109466386 (for QYrCW357-3DL), and AX-109995005 (for QYrCW357-6BS) were evaluated in a diversity panel including 225 wheat cultivars and breeding lines. These results suggested that these high-throughput markers could be used to introduce QYrCW357-1BL, QYrCW357-2AL, QYrCW357-3DL, and QYrCW357-6BS into commercial wheat cultivars. Combinations of these genes with other APR QTL should lead to higher levels of stripe rust resistance along with the beneficial effects of multi-disease resistance gene Yr29 on improving resistance to other diseases.

CRISPR-Cas12a-Based Diagnostics of Wheat Fungal Diseases

Fusarium head blight (FHB) of wheat, mainly caused by Fusarium graminearum (F. graminearum) infection, reduces crop yield and contaminates grain with mycotoxins. We report a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a-based nucleic acid assay for an early and rapid diagnosis of wheat FHB. Guide RNA (gRNA) was screened for highly specific recognition of polymerase chain reaction (PCR) amplicon of the internal transcribed spacer (ITS) region and the transcription elongation factor 1α (EF1α) of F. graminearum. The trans-activation of Cas12a protein cleaves the single-stranded DNA probes with the terminal fluorophore and quencher groups, thus allowing us to report the presence of ITS and EF1α of F. graminearum. Owing to the dual recognition process through PCR primers and gRNA hybridization, the approach realized specific discrimination of F. graminearum from other pathogenic fungi. It also allowed us to detect as low as 1 fg/μL total DNA from F. graminearum, which is sufficient to diagnose a 4 day F. graminearum infection. CRISPR-Cas12a-based nucleic acid assay promises the molecular diagnosis of crop diseases and broadens the application of CRISPR tools.

A genome-wide association study revealed the genetic variation and candidate genes for grain copper content in bread wheat (Triticum aestivum L.)

As an essential microelement, copper plays a crucial role in the human body. However, the grains of bread wheat, a major crop food, contain a low copper content. Here, a diversity panel of 443 wheat accessions cultivated in four environments was used to analyse grain copper content by ICAP-7000, and the genetic variation in grain copper content was examined using a 660 K single nucleotide polymorphism chip. Phenotypic analysis indicated that the grain copper content varied between 2.58 mg kg^-1 and 13.65 mg kg^-1. A genome-wide association study identified 12 QTLs associated with grain copper content that showed significance in at least two environments on chromosomes 1A, 1D, 3D, 4A, 5A, 5D, 6B, 6D, 7A and 7D. Through haplotype analysis, the phenotypic difference between the haplotypes of three genes, TraesCS5D01G282300, TraesCS6B01G052900 and TraesCS7D01G146600, showed significance (P ⩽ 0.05) in four environments. They were considered to be important candidate genes for grain copper content in wheat. In addition, we detected that the grain copper content gradually decreased with release years among wheat accessions in China, and the percentage of favourable alleles showed a similar trend. Analysing the changes in grain copper content with yield factors, we found that the dilute effect was mainly caused by thousand kernel weight. This study provides useful information on the genetic basis for grain copper content, and thus helps in improving the wheat grain quality.

Genome-Wide Association Study on Root System Architecture and Identification of Candidate Genes in Wheat (Triticum aestivum L.)

The root tissues play important roles in water and nutrient acquisition, environmental adaptation, and plant development. In this study, a diversity panel of 388 wheat accessions was collected to investigate nine root system architecture (RSA) traits at the three-leaf stage under two growing environments: outdoor pot culture (OPC) and indoor pot culture (IPC). Phenotypic analysis revealed that root development was faster under OPC than that under IPC and a significant correlation was observed between the nine RSA traits. The 660K single-nucleotide polymorphism (SNP) chip was used for a genome-wide association study (GWAS). Significant SNPs with a threshold of −log10 (p-value) ≥ 4 were considered. Thus, 36 quantitative trait loci (QTLs), including 13 QTL clusters that were associated with more than one trait, were detected, and 31 QTLs were first identified. The QTL clusters on chromosomes 3D and 5B were associated with four and five RSA traits, respectively. Two candidate genes, TraesCS2A01G516200 and TraesCS7B01G036900, were found to be associated with more than one RSA trait using haplotype analysis, and preferentially expressed in the root tissues. These favourable alleles for RSA traits identified in this study may be useful to optimise the root system in wheat.

Enhanced stripe rust resistance obtained by combining Yr30 with a widely dispersed, consistent QTL on chromosome arm 4BL

YrFDC12 and PbcFDC, co-segregated in chromosome 4BL, and significantly interacted with Yr30/Pbc1 to enhance stripe rust resistance and to promote pseudo-black chaff development. Cultivars with durable resistance are the most popular means to control wheat stripe rust. Durable resistance can be achieved by stacking multiple adult plant resistance (APR) genes that individually have relatively small effect. Chinese wheat cultivars Ruihua 520 (RH520) and Fengdecun 12 (FDC12) confer partial APR to stripe rust across environments. One hundred and seventy recombinant inbred lines from the cross RH520 × FDC12 were used to determine the genetic basis of resistance and identify genomic regions associated with stripe rust resistance. Genotyping was carried out using 55 K SNP array, and eight quantitative trait loci (QTL) were detected on chromosome arms 2AL, 2DS, 3BS, 4BL, 5BL (2), and 7BL (2) by inclusive composite interval mapping. Only QYr.nwafu-3BS from RH520 and QYr.nwafu-4BL.2 (named YrFDC12 for convenience) from FDC12 were consistent across the four testing environments. QYr.nwafu-3BS is likely the pleiotropic resistance gene Sr2/Yr30. YrFDC12 was mapped in a 2.1-cM interval corresponding to 12 Mb and flanked by SNP markers AX-111121224 and AX-89518393. Lines harboring both Yr30 and YrFDC12 displayed higher resistance than the parents and expressed pseudo-black chaff (PBC) controlled by loci Pbc1 and PbcFDC12, which co-segregated with Yr30 and YrFDC12, respectively. Both marker-based and pedigree-based kinship analyses revealed that YrFDC12 was inherited from founder parent Zhou 8425B. Fifty-four other wheat cultivars shared the YrFDC12 haplotype. These results suggest an effective pyramiding strategy to acquire highly effective, durable stripe rust resistance in breeding.

Clinical outcomes of keratinized mucosa augmentation in jaws reconstructed with fibula or iliac bone flaps

This prospective study was undertaken to evaluate the treatment outcomes of keratinized mucosa augmentation (KMA) on the buccal and palatal/lingual sides of implants in jaws reconstructed after oncological surgery. Forty-two implants in 12 patients whose jaws had been reconstructed with a fibula or iliac bone flap were included. KMA was performed at 3 months after implant placement; this included an apically displaced partial-thickness flap and a free gingival graft (FGG) around the implants to increase the keratinized mucosa width (KMW). Patients were followed up for at least 6 months post-surgery. KMW, shrinkage, and patient pain and discomfort measured on a visual analogue scale were analysed. A histological analysis was performed of tissue epithelium from two patients. The results showed that KMW was >2 mm on both the buccal and palatal/lingual sides during follow-up. Before surgery, histological analysis showed epithelium with no epithelial spikes; normal keratinized epithelial spikes were observed at 8 weeks after KMA. Greater KMW was observed around implants in reconstructed maxillae than around those in reconstructed mandibles (P < 0.001). Patients felt more pain at the donor site than at the recipient site during the first 3 days post-surgery. KMA with FGG was predictable in reconstructed jaws and may help maintain the long-term stability of implants.

LINC00174 triggers the malignant development of breast cancer by negatively regulating miR-1827 level

OBJECTIVE

Long non-coding RNAs (lncRNAs) are extensively involved in tumor development. In-depth researches on cancer-associated lncRNAs provide a theoretical basis for developing prognostic hallmarks and individualized therapeutic targets in breast cancer (BCa). This study aims to detect expression characteristics of LINC00174 in BCa and its biological role in regulating BCa cell phenotypes.

PATIENTS AND METHODS

LINC00174 levels in BCa and adjacent normal tissues were detected by quantitative real-time polymerase chain reaction (qRT-PCR). The influence of LINC00174 on pathological indicators of BCa was analyzed. In MCF-7 and MDA-MB-231 cells with LINC00174 knockdown, proliferative and migratory abilities were examined by cell counting kit-8 (CCK-8), colony formation and transwell assay, respectively. At last, molecular mechanisms of LINC00174 and its downstream gene miR-1827 in regulating BCa development were explored by Luciferase assay and rescue experiments.

RESULTS

LINC00174 was upregulated in BCa tissues than adjacent normal ones. High level of LINC00174 predicted advanced tumor staging, high metastasis rate and poor prognosis in BCa. Knockdown of LINC00174 attenuated proliferative and migratory abilities in BCa cells. MiR-1827 was the target gene binding LINC00174, showing a negative correlation between each other. Silence of miR-1827 abolished the regulatory effects of LINC00174 on proliferative and migratory abilities in BCa cells.

CONCLUSIONS

LINC00174 is upregulated in BCa samples. It is closely linked to tumor staging, metastasis and prognosis in BCa. By negatively regulating miR-1827 level, LINC00174 aggravates the malignant development of BCa.

Machine learning from quantitative coronary computed tomography angiography predicts ischemia and impaired myocardial blood flow

Background

Atherosclerotic plaque characteristics influence the hemodynamic consequences of coronary lesions. This study sought to assess the performance of a machine learning (ML) score integrating coronary computed tomography angiography (CCTA)-based quantitative plaque features for the prediction of ischemia by invasive fractional flow reserve (FFR) and impaired myocardial blood flow (MBF) by [15O]H2O positron emission tomography (PET).

Methods

This post-hoc analysis of the PACIFIC (Prospective Comparison of Cardiac PET/CT, SPECT/CT Perfusion Imaging and CT Coronary Angiography With Invasive Coronary Angiography) trial included 208 patients with suspected coronary artery disease who underwent CCTA, [15O]H2O PET, and 3-vessel invasive FFR. Plaque quantification from CCTA was performed using semiautomated software. A boosted ensemble ML algorithm (XGBoost) trained on data from the NXT (Analysis of Coronary Blood Flow using CT Angiography: Next Steps) trial was used to develop a ML score for the prediction of per-vessel ischemia (invasive FFR ≤0.80). The performance of the ML score was evaluated in 551 vessels from the PACIFIC trial for external validation. Thereafter, we assessed the discriminative ability of the ML score for per-vessel impaired hyperemic MBF (≤2.30 mL/min/g).

Results

In total, 138 (25.0%) vessels had ischemia and 195 (35.4%) vessels had impaired hyperemic MBF. CCTA-derived quantitative percent diameter stenosis and low-density noncalcified plaque (LDNCP) volume were higher in ischemic vessels compared with non-ischemic vessels (60.8% vs. 19.9%; and 42.3 mm3 vs. 9.1 mm3; both p&lt;0.001). The ML score demonstrated a significantly higher area under the receiver-operating characteristic curve (AUC) for predicting ischemia (0.92, 95% confidence interval [CI] 0.89–0.94) compared with visual stenosis grade (0.84, 95% CI 0.80–0.87; p&lt;0.001). Overall, quantitative percent diameter stenosis and LDNCP volume had greatest feature importance for ML, followed by percent area stenosis, minimum luminal diameter, and contrast density drop (Figure 1). An individualized explanation of ML ischemia prediction is shown in Figure 2. When applied for impaired MBF discrimination, the ML score exhibited an AUC of 0.82 (95% CI 0.78–0.85) and was superior to visual stenosis grade (AUC 0.76, 95% CI 0.72–0.80; p=0.03).

Conclusions

An externally validated ML score integrating CCTA-based quantitative plaque features accurately predicts FFR-defined ischemia and abnormal MBF by PET, outperforming standard visual CCTA interpretation.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Heart, Lung, and Blood Institute, United States Performance of the ML scoreIndividual explanation of ML prediction

[Trajectories of body mass index Z-score and risk of high blood pressure in late adolescence in Suzhou children]

Objective: To identify age and gender standardized body mass index among children and adolescents and explore their associations with high blood pressure (HBP) in late adolescence. Methods: The current study was based on the Health Promotion Program for Children and Adolescents, school-based surveillance successively conducted from 2012 to 2019 in Suzhou, China. A total of 11 812 children and adolescents aged 16-18 years, who had ≥4 examination records during 2012-2018 and were also involved in a surveillance program in 2019, were included. Latent class growth mixture modeling was used to identify the BMI-Z trajectories in different genders, and multivariate logistic regression was used to analyze the associations between different BMI-Z trajectories and risk of HBP in late adolescence. Results: Six distinct BMI-Z trajectories were determined for both genders:thin, slightly thin,standard, declining, overweight, and obese. Compared with the regular group, the obesity group had 94.0% (OR=1.94, 95%CI: 1.43-2.63) and 107.0% (OR=2.07, 95%CI: 1.33-3.22) increased risk of developing HBP in late adolescence in boys and girls, respectively. However, a neutral association was found between the descending group and HBP in late adolescence. Conclusions: Persistent obesity in children may increase the risk of HBP in their late adolescence. If an obese child restores normal weight before late adolescence, the risk of HBP may reduce.