Effect of genotyping errors on linkage map construction based on repeated chip analysis of two recombinant inbred line populations in wheat (Triticum aestivum L.).

Linkage maps are essential for genetic mapping of phenotypic traits, gene map-based cloning, and marker-assisted selection in breeding applications. Construction of a high-quality saturated map requires high-quality genotypic data on a large number of molecular markers. Errors in genotyping cannot be completely avoided, no matter what platform is used. When genotyping error reaches a threshold level, it will seriously affect the accuracy of the constructed map and the reliability of consequent genetic studies. In this study, repeated genotyping of two recombinant inbred line (RIL) populations derived from crosses Yangxiaomai × Zhongyou 9507 and Jingshuang 16 × Bainong 64 was used to investigate the effect of genotyping errors on linkage map construction. Inconsistent data points between the two replications were regarded as genotyping errors, which were classified into three types. Genotyping errors were treated as missing values, and therefore the non-erroneous data set was generated. Firstly, linkage maps were constructed using the two replicates as well as the non-erroneous data set. Secondly, error correction methods implemented in software packages QTL IciMapping (EC) and Genotype-Corrector (GC) were applied to the two replicates. Linkage maps were therefore constructed based on the corrected genotypes and then compared with those from the non-erroneous data set. Simulation study was performed by considering different levels of genotyping errors to investigate the impact of errors and the accuracy of error correction methods. Results indicated that map length and marker order differed among the two replicates and the non-erroneous data sets in both RIL populations. For both actual and simulated populations, map length was expanded as the increase in error rate, and the correlation coefficient between linkage and physical maps became lower. Map quality can be improved by repeated genotyping and error correction algorithm. When it is impossible to genotype the whole mapping population repeatedly, 30% would be recommended in repeated genotyping. The EC method had a much lower false positive rate than did the GC method under different error rates. This study systematically expounded the impact of genotyping errors on linkage analysis, providing potential guidelines for improving the accuracy of linkage maps in the presence of genotyping errors.

The TaSOC1-TaVRN1 module integrates photoperiod and vernalization signals to regulate wheat flowering.

Wheat needs different durations of vernalization, which accelerates flowering by exposure to cold temperature, to ensure reproductive development at the optimum time, as that is critical for adaptability and high yield. TaVRN1 is the central flowering regulator in the vernalization pathway and encodes a MADS-box transcription factor (TF) that usually works by forming hetero- or homo-dimers. We previously identified that TaVRN1 bound to an MADS-box TF TaSOC1 whose orthologues are flowering activators in other plants. The specific function of TaSOC1 and the biological implication of its interaction with TaVRN1 remained unknown. Here, we demonstrated that TaSOC1 was a flowering repressor in the vernalization and photoperiod pathways by overexpression and knockout assays. We confirmed the physical interaction between TaSOC1 and TaVRN1 in wheat protoplasts and in planta, and further validated their genetic interplay. A Flowering Promoting Factor 1-like gene TaFPF1-2B was identified as a common downstream target of TaSOC1 and TaVRN1 through transcriptome and chromatin immunoprecipitation analyses. TaSOC1 competed with TaVRT2, another MADS-box flowering regulator, to bind to TaVRN1; their coding genes synergistically control TaFPF1-2B expression and flowering initiation in response to photoperiod and low temperature. We identified major haplotypes of TaSOC1 and found that TaSOC1-Hap1 conferred earlier flowering than TaSOC1-Hap2 and had been subjected to positive selection in wheat breeding. We also revealed that wheat SOC1 family members were important domestication loci and expanded by tandem and segmental duplication events. These findings offer new insights into the regulatory mechanism underlying flowering control along with useful genetic resources for wheat improvement.

Tectoridin alleviates caerulein-induced severe acute pancreatitis by targeting ERK2 to promote macrophage M2 polarization.

Severe acute pancreatitis (SAP) is an inflammatory disease of the pancreas with a high mortality rate. Macrophages play a crucial role in the pathogenesis of pancreatitis. Tectoridin (Tec) is a highly active isoflavone with anti-inflammatory pharmacological activity. However, the role of Tec in the SAP process is not known. The purpose of this study was to investigate the therapeutic effect and potential mechanism of Tec on SAP. To establish SAP mice by intraperitoneal injection of caerulein and Lipopolysaccharide (LPS), the role of Tec in the course of SAP was investigated based on histopathology, biochemical indicators of amylase and lipase and inflammatory factors. The relationship between Tec and macrophage polarization was verified by immunofluorescence, real-time quantitative PCR and Western blot analysis. We then further predicted the possible targets and signal pathways of action of Tec by network pharmacology and molecular docking, and validated them by in vivo and in vitro. In this study, we demonstrated that Tec significantly reduced pancreatic injury in SAP mice, and decreased serum levels of amylase and lipase. The immunofluorescence and Western blot analysis showed that Tec promoted macrophage M2 polarization. Network pharmacology and molecular docking predicted that Tec may target ERK2 for the treatment of SAP, and in vivo and in vitro experiments proved that Tec inhibited the ERK MAPK signal pathway. In summary, Tec can target ERK2, promote macrophage M2 polarization and attenuate pancreatic injury, Tec may be a potential drug for the treatment of SAP.

Correlation between the development of phage resistance and the original antibiotic resistance of host bacteria under the co-exposure of antibiotic and bacteriophage.

Bacteriophages (phages) are viruses capable of regulating the proliferation of antibiotic resistant bacteria (ARB). However, phages that directly cause host lethality may quickly select for phage resistant bacteria, and the co-evolutionary trade-offs under varying environmental conditions, including the presence of antibiotics, remains unclear as to their impact on phage and antibiotic resistance. Here, we report the emergence of phage resistance in three distinct E. coli strains with varying resistance to ß-lactam antibiotics, treated with different ampicillin (AMP) concentrations. Hosts exhibiting stronger antibiotic resistance demonstrated a higher propensity to develop and maintain stable phage resistance. When exposed to polyvalent phage KNT-1, the growth of AMP-sensitive E. coli K12 was nearly suppressed within 18 h, while the exponential growth of AMP-resistant E. coli TEM and super-resistant E. coli NDM-1 was delayed by 12 h and 8 h, respectively. The mutation frequency and mutated colony count of E. coli NDM-1 were almost unaffected by co-existing AMP, whereas for E. coli TEM and K12, these metrics significantly decreased with increasing AMP concentration from 8 to 50 µg/mL, becoming unquantifiable at 100 µg/mL. Furthermore, the fitness costs of phage resistance mutation and its impact on initial antibiotic resistance in bacteria were further examined, through analyzing AMP susceptibility, biofilm formation and EPS secretion of the isolated phage resistant mutants. The results indicated that acquiring phage resistance could decrease antibiotic resistance, particularly for hosts lacking strong antibiotic resistance. The ability of mutants to form biofilm contributes to antibiotic resistance, but the correlation is not entirely positive, while the secretion of extracellular polymeric substance (EPS), especially the protein content, plays a crucial role in protecting the bacteria from both antibiotic and phage exposure. This study explores phage resistance development in hosts with different antibiotic resistance and helps to understand the limitations and possible solutions of phage-based technologies.

The safety of benzodiazepines and related drugs during pregnancy: an updated meta-analysis of cohort studies.

PURPOSE: The prevalence of benzodiazepines and related drugs (BZRDs) use during pregnancy increased sharply in recent years. Thus, there are concerns regarding the pregnancy outcomes following exposure to BZRDs. METHODS: Two electronic databases were thoroughly searched to identify related clinical studies published from inception until June 2023. English-language cohort studies with high-quality comparing antenatal BZRDs exposure to an unexposed group on any delivery outcome were included. RESULTS: Ten cohort studies that estimated adverse neonatal outcomes associated with exposure to BZRDs during pregnancy were included. Exposure to BZRDs during pregnancy was associated with an increased risk of congenital malformation [odds ratio (OR) 1.09, 95% confidence interval (CI) 1.05-1.13, p < 0.001], heart malformation (OR 1.13, 95% CI 1.04-1.22, p = 0.003), preterm birth (OR 1.45, 95% CI 1.23-1.7, p < 0.001), SGA (OR 1.18, 95% CI 1.08-1.29, P < 0.001), LBW (OR 1.42, 95% CI 1.25-1.6, p = 0.001) or low Apgar score (OR 1.42, 95% CI 1.08-1.87, p = 0.011),compared with no exposure. Further analyses limited to the first trimester exposure yielded consistent results. CONCLUSIONS: Exposure to BZRDs during pregnancy may be associated with several adverse neonatal outcomes. However, we could not rule out the potential indication confounding factor, further studies with high-quality that control for important confounders are still needed to verify our findings.

Efficient proteome-wide identification of transcription factors targeting Glu-1: A case study for functional validation of TaB3-2A1 in wheat.

High-molecular-weight glutenin subunits (HMW-GS), a major component of seed storage proteins (SSP) in wheat, largely determine processing quality. HMW-GS encoded by GLU-1 loci are mainly controlled at the transcriptional level by interactions between cis-elements and transcription factors (TFs). We previously identified a conserved cis-regulatory module CCRM1-1 as the most essential cis-element for Glu-1 endosperm-specific high expression. However, the TFs targeting CCRM1-1 remained unknown. Here, we built the first DNA pull-down plus liquid chromatography-mass spectrometry platform in wheat and identified 31 TFs interacting with CCRM1-1. TaB3-2A1 as proof of concept was confirmed to bind to CCRM1-1 by yeast one hybrid and electrophoretic mobility shift assays. Transactivation experiments demonstrated that TaB3-2A1 repressed CCRM1-1-driven transcription activity. TaB3-2A1 overexpression significantly reduced HMW-GS and other SSP, but enhanced starch content. Transcriptome analyses confirmed that enhanced expression of TaB3-2A1 down-regulated SSP genes and up-regulated starch synthesis-related genes, such as TaAGPL3, TaAGPS2, TaGBSSI, TaSUS1 and TaSUS5, suggesting that it is an integrator modulating the balance of carbon and nitrogen metabolism. TaB3-2A1 also had significant effects on agronomic traits, including heading date, plant height and grain weight. We identified two major haplotypes of TaB3-2A1 and found that TaB3-2A1-Hap1 conferred lower seed protein content, but higher starch content, plant height and grain weight than TaB3-2A1-Hap2 and was subjected to positive selection in a panel of elite wheat cultivars. These findings provide a high-efficiency tool to detect TFs binding to targeted promoters, considerable gene resources for dissecting regulatory mechanisms underlying Glu-1 expression, and a useful gene for wheat improvement.

Rht12b, a widely used ancient allele of TaGA2oxA13, reduces plant height and enhances yield potential in wheat.

KEY MESSAGE: We identified a new wheat dwarfing allele Rht12b conferring reduced height and higher grain yield, pinpointed its causal variations, developed a breeding-applicable marker, and traced its origin and worldwide distribution. Plant height control is essential to optimize lodging resistance and yield gain in crops. RHT12 is a reduced height (Rht) locus that is identified in a mutationally induced dwarfing mutant and encodes a gibberellin 2-oxidase TaGA2oxA13. However, the artificial dwarfing allele is not used in wheat breeding due to excessive height reduction. Here, we confirmed a stable Rht locus, overlapping with RHT12, in a panel of wheat cultivars and its dwarfing allele reduced plant height by 5.4-8.2 cm, equivalent to Rht12b, a new allele of RHT12. We validated the effect of Rht12b on plant height in a bi-parent mapping population. Importantly, wheat cultivars carrying Rht12b had higher grain yield than those with the contrasting Rht12a allele. Rht12b conferred higher expression level of TaGA2oxA13. Transient activation assays defined SNP-390(C/A) in the promoter of TaGA2oxA13 as the causal variation. An efficient kompetitive allele-specific PCR marker was developed to diagnose Rht12b. Conjoint analysis showed that Rht12b plus the widely used Rht-D1b, Rht8 and Rht24b was the predominant Rht combination and conferred a moderate plant height in tested wheat cultivars. Evolutionary tracking uncovered that RHT12 locus arose from a tandem duplication event with Rht12b firstly appearing in wild emmer. The frequency of Rht12b was approximately 70% (700/1005) in a worldwide wheat panel and comparable to or higher than those of other widely used Rht genes, suggesting it had been subjected to positive selection. These findings not only identify a valuable Rht gene for wheat improvement but also develop a functionally diagnostic tool for marker-assisted breeding.

Genetic dissection of grain morphology and yield components in a wheat line with defective grain filling.

KEY MESSAGE: We identified stable QTL for grain morphology and yield component traits in a wheat defective grain filling line and validated genetic effects in a panel of cultivars using breeding-relevant markers. Grain filling capacity is essential for grain yield and appearance quality in cereal crops. Identification of genetic loci for grain filling is important for wheat improvement. However, there are few genetic studies on grain filling in wheat. Here, a defective grain filling (DGF) line wdgf1 characterized by shrunken grains was identified in a population derived from multi-round crosses involving nine parents and a recombinant inbreed line (RIL) population was generated from the cross between wdgf1 and a sister line with normal grains. We constructed a genetic map of the RIL population using the wheat 15K single nucleotide polymorphism chip and detected 25 stable quantitative trait loci (QTL) for grain morphology and yield components, including three for DGF, eleven for grain size, six for thousand grain weight, three for grain number per spike and two for spike number per m2. Among them, QDGF.caas-7A is co-located with QTGW.caas-7A and can explain 39.4-64.6% of the phenotypic variances, indicating that this QTL is a major locus controlling DGF. Sequencing and linkage mapping showed that TaSus2-2B and Rht-B1 were candidate genes for QTGW.caas-2B and the QTL cluster (QTGW.caas-4B, QGNS.caas-4B, and QSN.caas-4B), respectively. We developed kompetitive allele-specific PCR markers tightly linked to the stable QTL without corresponding to known yield-related genes, and validated their genetic effects in a diverse panel of wheat cultivars. These findings not only lay a solid foundation for genetic dissection underlying grain filling and yield formation, but also provide useful tools for marker-assisted breeding.

Fine mapping and characterization of a major QTL for plant height on chromosome 5A in wheat.

KEY MESSAGE: We precisely mapped QPH.caas-5AL for plant height in wheat, predicted candidate genes and confirmed genetic effects in a panel of wheat cultivars. Plant height is an important agronomic trait, and appropriately reduced height can improve yield potential and stability in wheat, usually combined with sufficient water and fertilizer. We previously detected a stable major-effect quantitative trait locus QPH.caas-5AL for plant height on chromosome 5A in a recombinant inbred line population of the cross 'Doumai × Shi 4185' using the wheat 90 K SNP assay. Here , QPH.caas-5AL was confirmed using new phenotypic data in additional environment and new-developed markers. We identified nine heterozygous recombinant plants for fine mapping of QPH.caas-5AL and developed 14 breeder-friendly kompetitive allele-specific PCR markers in the region of QPH.caas-5AL based on the genome re-sequencing data of parents. Phenotyping and genotyping analyses of secondary populations derived from the self-pollinated heterozygous recombinant plants delimited QPH.caas-5AL into an approximate 3.0 Mb physical region (521.0-524.0 Mb) according to the Chinese Spring reference genome. This region contains 45 annotated genes, and six of them were predicted as the candidates of QPH.caas-5AL based on genome and transcriptome sequencing analyses. We further validated that QPH.caas-5AL has significant effects on plant height but not yield component traits in a diverse panel of wheat cultivars; its dwarfing allele is frequently used in modern wheat cultivars. These findings lay a solid foundation for the map-based cloning of QPH.caas-5AL and also provide a breeding-applicable tool for its marker-assisted selection. Keymessage We precisely mapped QPH.caas-5AL for plant height in wheat, predicted candidate genes and confirmed genetic effects in a panel of wheat cultivars.

Polarization-insensitive 90° optical hybrid using silica-based PLC.

A 90° optical hybrid (OH) based on a 4×4 multimode interference (MMI) coupler is characterized and analyzed using the silica-based planar light circuit. The OH is designed to be polarization-insensitive with an extremely low polarization-dependent loss (<0.18d B) and phase error (w i t h i n±1.3∘). The fabricated chip exhibits an excess loss of 3.4 dB and 3.8 dB for TE and TM polarizations at 1550 nm. The measured phase error is w i t h i n±7.2∘ over 50 nm in the C+L band with a polarization-dependent error w i t h i n±3.5∘. The fabrication tolerance of the MMI width and waveguide sidewall angle is analyzed, which can well explain the deviation from the theoretical calculation.

Hypertension in pregnancy as a risk factor for placenta accreta spectrum: a systematic review incorporating a network meta-analysis.

BACKGROUND: A meta-analysis was performed to evaluate the potential effects of hypertension in pregnancy on the placenta accreta spectrum. METHODS: A systematic literature search in OVID, Embase, Cochrane Library, PubMed, and Google Scholar up to May 2021 was done, and six studies were found including 126,224 pregnant women; 7164 of them had hypertension in pregnancy and 816 had placenta accreta spectrum. They were reporting relationships between the potential effects of hypertension in pregnancy on the placenta accreta spectrum. The odds ratio (OR) with 95% confidence intervals (CIs) was calculated to assess the potential effects of hypertension in pregnancy on the placenta accreta spectrum using the dichotomous with a random- or fixed-effect model. RESULTS: Pregnancy-induced hypertension was significantly related to lower prevalence of placenta accreta spectrum (OR 0.56; 95% CI 0.37-0.84, p = 0.005) with no heterogeneity (I2 = 0%) compared to control (no hypertension in pregnancy). When looking at the result comparing the prevalence of hypertension in pregnancy in women with placenta accrete compared to control (no placenta accrete), we found that the placenta accreta spectrum was significantly related to lower prevalence of hypertension in pregnancy (OR 0.65; 95% CI 0.43-0.98, p = 0.04) compared to control. CONCLUSIONS: Hypertension in pregnancy may have a lower prevalence of placenta accrete. Further studies are required to validate these findings.

Phosphogypsum/titanium gypsum coupling for enhanced biochar immobilization of lead: Mineralization reaction behavior and electron transfer effect.

The hazards caused by Pb pollution have received worldwide attention. Phosphogypsum (PG) and titanium gypsum (TG) have the disadvantage of limited adsorption capacity and poor dispersion when used as heavy metal adsorbents on their own. The excellent pore and electron transfer capacity of biochar makes it possible to combine with PG and TG to solidify/stabilize Pb2+. In this study, the mechanism of Pb2+ adsorption/immobilization by rice husk biochar (BC) combined with PG/TG was investigated in terms of both mineral formation and electron transfer rate. The removal rate of Pb2+ by BC composite PG (BC/PG-Pb) or TG (BC/TG-Pb) was as high as 97%-98%, an increase of 120.9% and 122.5% over BC. Adsorption kinetics and mineral precipitation results indicate that the main removal of Pb2+ from BC/PG-Pb and BC/TG-Pb is achieved by PG/TG induced Pb-sulfate and Pb-phosphate formation. The addition of PG/TG significantly enhances the formation of stable Pb-minerals on the biochar surface, with the proportion of non-bioaccessible forms exceeding 50%. The four-step extraction results confirm that P and F in PG/TG are key in facilitating the conversion of Pb minerals to pyromorphite. The rich pore structure of biochar not only disperses the easily agglomerated PG/TG onto the biochar surface, but also attracts Pb2+ for uniformly dispersed precipitation. Furthermore, the excellent electrical conductivity and smooth electron transfer channels of biochar facilitate the reaction rate of Pb2+ mineralization. Overall, the use of biochar in combination with PG/TG is a promising technology for the combination of solid waste resourceisation and Pb remediation.

[Postoperative Sleep Disturbance in Patients Undergoing Arthroplasty: Risk Prediction Modeling Based on Logistic Regression].

Objective: To construct a risk predictive model for postoperative sleep disturbance (PSD) in patients undergoing arthroplasty by using logistic regression. Methods: We retrospectively collected the data of 4286 patients who underwent joint replacement surgeries at a tertiary-care hospital in Chengdu, China between January 1, 2017 and September 30, 2021. With 3001 cases in the training set and 1285 cases in the test set, we constructed the model by using a logistic regression algorithm to screen for predictors in Matlab, displaying the predicted risks of postoperative sleep disturbance with nomographs. The performance of the model was assessed by the area under the curve ( AUC) of the receiver operating characteristic curve, accuracy, precision, recall, F1 value, and calibration curve. Results: A total of 9 predictors, including post-admission preoperative sleep disturbance, ward type, body mass index, smoking status, range of diseases, joint mobility (flexion), joint mobility (extension), preoperative last hemoglobin, and type of surgery, were eventually included in the study for predictive modeling . The performance assessment findings of the predictive model were as follows, AUC value, 0.708 (95% confidence interval: 0.677-0.740), accuracy, 75.20%, precision, 65.80%, recall, 43.70%, and F1 value, 0.525. The calibration curve showed good agreement between the predicted probabilities and the actual data. Conclusion: The model constructed in the study has good predictive efficacy and the nomographs are simple and easy to use. With this model, health workers can make preoperative prediction of the risk of PSD in arthroplasty patients based on the predictors, which facilitates early prevention and reduces the risk of postoperative sleep disturbance in patients.

[First-Class Nursing Discipline Construction Spearheads the Cultivation of First-Class Talents].

Cultivating first-class talents is a key task of the Double First-Class Initiative, a national plan to build a number of world-class universities and disciplines in China by the end of 2050. On the basis of reviewing the history of the development of the nursing discipline, we analyzed, herein, opportunities and challenges of nursing professional training under the strategic guidance of the Double First-Class Initiative. We proposed suggestions on the cultivation of first-class nursing professionals of the future by considering the following aspects, constructing a theoretical system of ideological and political education for nursing education with Chinese characteristics, exploring for ways to develop a nursing knowledge system and personnel training model around the axis of a life-course approach to health, building "nursing plus" interdisciplinary clusters to cultivate innovative talents with interdisciplinary integrated abilities, enhancing efforts to recruit and cultivate scientific and technological talents, optimizing in an all-round way the composition of qualified nursing personnel, gaining the support of first-class research platforms, and creating incubation centers for innovative and outstanding nursing professionals.

[Deep Learning-Based Identification of Common Complication Features of Surgical Incisions].

Objective: In recent years, due to the development of accelerated recovery after surgery and day surgery in the field of surgery, the average length-of-stay of patients has been shortened and patients stay at home for post-surgical recovery and healing of the surgical incisions. In order to identify, in a timely manner, the problems that may appear at the incision site and help patients prevent or reduce the anxiety they may experience after discharge, we used deep learning method in this study to classify the features of common complications of surgical incisions, hoping to realize patient-directed early identification of complications common to surgical incisions. Methods: A total of 1 224 postoperative photographs of patients' surgical incisions were taken and collected at a tertiary-care hospital between June 2021 and March 2022. The photographs were collated and categorized according to different features of complications of the surgical incisions. Then, the photographs were divided into training, validation, and test sets at the ratio of 8∶1∶1 and 4 types of convolutional neural networks were applied in the training and testing of the models. Results: Through the training of multiple convolutional neural networks and the testing of the model performance on the basis of a test set of 300 surgical incision images, the average accuracy of the four ResNet classification network models, SE-ResNet101, ResNet50, ResNet101, and SE-ResNet50, for surgical incision classification was 0.941, 0.903, 0.896, and 0.918, respectively, the precision was 0.939, 0.898, 0.868, and 0.903, respectively, and the recall rate was 0.930, 0.880, 0.850, and 0.894, respectively, with the SE-Resnet101 network model showing the highest average accuracy of 0.941 for incision feature classification. Conclusion: Through the combined use of deep learning technology and images of surgical incisions, problematic features of surgical incisions can be effectively identified by examining surgical incision images. It is expected that patients will eventually be able to perform self-examination of surgical incisions on smart terminals.

Evolution patterns of NBS genes in the genus Dendrobium and NBS-LRR gene expression in D. officinale by salicylic acid treatment.

BACKGROUND: Dendrobium officinale Kimura et Migo, which contains rich polysaccharides, flavonoids and alkaloids, is a Traditional Chinese Medicine (TCM) with important economic benefits, while various pathogens have brought huge losses to its industrialization. NBS gene family is the largest class of plant disease resistance (R) genes, proteins of which are widely distributed in the upstream and downstream of the plant immune systems and are responsible for receiving infection signals and regulating gene expression respectively. It is of great significance for the subsequent disease resistance breeding of D. officinale to identify NBS genes by using the newly published high-quality chromosome-level D. officinale genome. RESULTS: In this study, a total of 655 NBS genes were uncovered from the genomes of D. officinale, D. nobile, D. chrysotoxum, V. planifolia, A. shenzhenica, P. equestris and A. thaliana. The phylogenetic results of CNL-type protein sequences showed that orchid NBS-LRR genes have significantly degenerated on branches a and b. The Dendrobium NBS gene homology analysis showed that the Dendrobium NBS genes have two obvious characteristics: type changing and NB-ARC domain degeneration. Because the NBS-LRR genes have both NB-ARC and LRR domains, 22 D. officinale NBS-LRR genes were used for subsequent analyses, such as gene structures, conserved motifs, cis-elements and functional annotation analyses. All these results suggested that D. officinale NBS-LRR genes take part in the ETI system, plant hormone signal transduction pathway and Ras signaling pathway. Finally, there were 1,677 DEGs identified from the salicylic acid (SA) treatment transcriptome data of D. officinale. Among them, six NBS-LRR genes (Dof013264, Dof020566, Dof019188, Dof019191, Dof020138 and Dof020707) were significantly up-regulated. However, only Dof020138 was closely related to other pathways from the results of WGCNA, such as pathogen identification pathways, MAPK signaling pathways, plant hormone signal transduction pathways, biosynthetic pathways and energy metabolism pathways. CONCLUSION: Our results revealed that the NBS gene degenerations are common in the genus Dendrobium, which is the main reason for the diversity of NBS genes, and the NBS-LRR genes generally take part in D. officinale ETI system and signal transduction pathways. In addition, the D. officinale NBS-LRR gene Dof020138, which may have an important breeding value, is indirectly activated by SA in the ETI system.

Chest CT Patterns from Diagnosis to 1 Year of Follow-up in Patients with COVID-19.

Background The chest CT manifestations of COVID-19 from hospitalization to convalescence after 1 year are unknown. Purpose To assess chest CT manifestations of COVID-19 up to 1 year after symptom onset. Materials and Methods Patients were enrolled if they were admitted to the hospital because of COVID-19 and underwent CT during hospitalization at two isolation centers between January 27, 2020, and March 31, 2020. In a prospective study, three serial chest CT scans were obtained at approximately 3, 7, and 12 months after symptom onset and were longitudinally analyzed. The total CT score of pulmonary lobe involvement, ranging from 0 to 25, was assessed (score of 1-5 for each lobe). Univariable and multivariable logistic regression analyses were performed to explore independent risk factors for residual CT abnormalities after 1 year. Results A total of 209 study participants (mean age, 49 years ± 13 [standard deviation]; 116 women) were evaluated. CT abnormalities had resolved in 61% of participants (128 of 209) at 3 months and in 75% of participants (156 of 209) at 12 months. Among participants with chest CT abnormalities that had not resolved, there were residual linear opacities in 25 of the 209 participants (12%) and multifocal reticular or cystic lesions in 28 of the 209 participants (13%). Age 50 years or older, lymphopenia, and severe or aggravation of acute respiratory distress syndrome were independent risk factors for residual CT abnormalities at 1 year (odds ratios = 15.9, 18.9, and 43.9, respectively; P < .001 for each comparison). In 53 participants with residual CT abnormalities at 12 months, reticular lesions (41 of 53 participants [77%]) and bronchial dilation (39 of 53 participants [74%]) were observed at discharge and were persistent in 28 (53%) and 24 (45%) of the 53 participants, respectively. Conclusion One year after COVID-19 diagnosis, chest CT scans showed abnormal findings in 53 of the 209 study participants (25%), with 28 of the 209 participants (13%) showing subpleural reticular or cystic lesions. Older participants with severe COVID-19 or acute respiratory distress syndrome were more likely to develop lung sequelae that persisted at 1 year. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Lee and Wi et al in this issue.

The association of obesity with the progression and outcome of COVID-19: The insight from an artificial-intelligence-based imaging quantitative analysis on computed tomography.

AIMS: To explore the association of obesity with the progression and outcome of coronavirus disease 2019 (COVID-19) at the acute period and 5-month follow-up from the perspectives of computed tomography (CT) imaging with artificial intelligence (AI)-based quantitative evaluation, which may help to predict the risk of obese COVID-19 patients progressing to severe and critical disease. MATERIALS AND METHODS: This retrospective cohort enrolled 213 hospitalized COVID-19 patients. Patients were classified into three groups according to their body mass index (BMI): normal weight (from 18.5 to <24 kg/m2 ), overweight (from 24 to <28 kg/m2 ) and obesity (≥28 kg/m2 ). RESULTS: Compared with normal-weight patients, patients with higher BMI were associated with more lung involvements in lung CT examination (lung lesions volume [cm3 ], normal weight vs. overweight vs. obesity; 175.5[34.0-414.9] vs. 261.7[73.3-576.2] vs. 395.8[101.6-1135.6]; p = 0.002), and were more inclined to deterioration at the acute period. At the 5-month follow-up, the lung residual lesion was more serious (residual total lung lesions volume [cm3 ], normal weight vs. overweight vs. obesity; 4.8[0.0-27.4] vs. 10.7[0.0-55.5] vs. 30.1[9.5-91.1]; p = 0.015), and the absorption rates were lower for higher BMI patients (absorption rates of total lung lesions volume [%], normal weight vs. overweight vs. obesity; 99.6[94.0-100.0] vs. 98.9[85.2-100.0] vs. 88.5[66.5-95.2]; p = 0.013). The clinical-plus-AI parameter model was superior to the clinical-only parameter model in the prediction of disease deterioration (areas under the ROC curve, 0.884 vs. 0.794, p < 0.05). CONCLUSIONS: Obesity was associated with severe pneumonia lesions on CT and adverse clinical outcomes. The AI-based model with combinational use of clinical and CT parameters had incremental prognostic value over the clinical parameters alone.

Fine mapping and characterization of a major QTL for grain weight on wheat chromosome arm 5DL.

KEY MESSAGE: We fine mapped QTL QTKW.caas-5DL for thousand kernel weight in wheat, predicted candidate genes and developed a breeding-applicable marker. Thousand kernel weight (TKW) is an important yield component trait in wheat, and identification of the underlying genetic loci is helpful for yield improvement. We previously identified a stable quantitative trait locus (QTL) QTKW.caas-5DL for TKW in a Doumai/Shi4185 recombinant inbred line (RIL) population. Here we performed fine mapping of QTKW.caas-5DL using secondary populations derived from 15 heterozygous recombinants and delimited the QTL to an approximate 3.9 Mb physical interval from 409.9 to 413.8 Mb according to the Chinese Spring (CS) reference genome. Analysis of genomic synteny showed that annotated genes in the physical interval had high collinearity among CS and eight other wheat genomes. Seven genes with sequence variation and/or differential expression between parents were predicted as candidates for QTKW.caas-5DL based on whole-genome resequencing and transcriptome assays. A kompetitive allele-specific PCR (KASP) marker for QTKW.caas-5DL was developed, and genotyping confirmed a significant association with TKW but not with other yield component traits in a panel of elite wheat cultivars. The superior allele of QTKW.caas-5DL was frequent in a panel of cultivars, suggesting that it had undergone positive selection. These findings not only lay a foundation for map-based cloning of QTKW.caas-5DL but also provide an efficient tool for marker-assisted selection.

Multimodal Imaging Response after the Singular or Combination Treatments of Vascular Endothelial Growth Factor Inhibitor and Immune Checkpoint Inhibitor.

This study aims to dynamically assess tumor changes after variable treatments with vascular endothelial growth factor (VEGF) inhibitor and/or immune checkpoint inhibitor (ICI) using multimodal imaging of MRI and 18F-FDG PET/CT in a hepatocellular carcinoma (HCC) mice model. Based on different treatments, 24 mice were randomly divided into four groups: control (isotype-matched IgG antibody 10 mg/kg), VEGF inhibitor (sorafenib 50 mg/kg), ICI (anti-PD-L1 antibody 10 mg/kg), and combination groups (sorafenib 50 mg/kg + anti-PD-L1 antibody 10 mg/kg). Quantitative imaging assessments, including volume transfer constant (Ktrans), apparent diffusion coefficient (ADC), lactate/choline ratio, and the maximum standardized 18F-FDG uptake value ratio of tumor to muscle (SUVtumor/SUVmuscle ratio), were acquired at different time points (before treatment and 7, 14, and 21 days after treatment). Quantitative data were presented as the mean ± standard errors and two-way repeated-measure ANOVA tests were performed for intergroup and intertime point comparisons. After 21 days from the initiation of therapies, combination group showed the lowest tumor volume and weight, followed by ICI, VEGF inhibitor, and control group, with no significance between the VEGF inhibitor and control groups. In addition, Ktrans values significantly decreased, and the lactate/choline ratio and SUVtumor/SUVmuscle ratio were significantly elevated in the VEGF inhibitor group. ADC significantly increased in the ICI and combination groups, with no significant differences in ADC observed between the control and VEGF inhibitor groups, which showed a similar dynamic change to the tumor volume. Furthermore, Ktrans, lactate/choline ratio, and ADC were significantly correlated with CD31+ area, hypoxyprobe+ area, and apoptosis, respectively. Our results suggest that the singular treatment and combination of the VEGF inhibitor and ICI treatments for HCC present different multimodal imaging changes in accordance with the specific histopathological features. These findings might facilitate the formulation of better treatment response criteria; besides, we find ADC is probably an indicator easily to obtain for treatment response evaluation.