Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process

The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.

[Clinical and electrophysiological characteristics and treatment outcomes of anti-neutrophil cytoplasmic antibody ANCA-associated vasculitic neuropathy]

Objective: To investigate the clinical and electrophysiological characteristics of ANCA-associated vasculitic neuropathy (VN) and analyze the predictors of treatment outcomes. Methods: Retrospective case series. In all, 652 consecutive patients with ANCA-associated vasculitis were admitted to the First Medical Center of the Chinese PLA General Hospital between January 2006 and December 2022. Peripheral neuropathy occurred in 91 patients. Patients were excluded if other known causes of neuropathy were present. Sixty-one patients were eventually enrolled, including 17 with eosinophilic granulomatosis with polyangiitis (EGPA), 11 with granulomatosis polyangiitis (GPA), and 33 with microscopic polyangiitis (MPA). Their clinical data were collected and clinical characteristics, VN manifestations, electrophysiological findings (including interside amplitude ratio [IAR]), and treatment outcomes were compared among the three subsets of AAV. Then, factors influencing the treatment outcomes were analyzed using multivariable logistic regression analysis. Results: Peripheral neuropathy occurred in 62.1%(18/29) of EGPA, 8.3%(15/180) of GPA, and 13.1%(58/443) of MPA patients. The age at onset and examination was higher in patients with MPA than those with EGPA or GPA (P<0.01). The occurrence of VN was later in patients with GPA than those with EGPA (P<0.01), and the GPA group had fewer affected nerves than the other two groups (P<0.016). The abnormal IARs of motor nerves in lower limbs were more detected in the EGPA than the MPA group (P<0.01). Logistic regression analysis suggested that higher Birmingham vasculitis activity score-version 3 (BVAS-V3) (OR=6.85, 95%CI 1.33-35.30) was associated with better treatment outcomes of VN. However, central nervous system involvement was a risk factor for poor treatment outcomes (OR=0.13, 95%CI 0.02-0.89). Conclusions: The clinical and electrophysiological characteristics of VN were slightly different among subsets of AAV. Patients with GPA often presented with polyneuropathy and had fewer nerves affected; mononeuritis multiplex was more common in EGPA than GPA and MPA. Higher BVAS-V3 and central nervous system involvement might predict the treatment outcome of VN.

Targeted long-read sequencing for comprehensive detection of CYP21A2 mutations in patients with 21-hydroxylase deficiency

BACKGROUND

21-Hydroxylase deficiency (21-OHD) is caused by pathogenic CYP21A2 variations. CYP21A2 is arranged in tandem with its highly homologous pseudogene CYP21A1P; therefore, it is prone to mismatch and rearrangement, producing different types of complex variations. There were few reports on using only one method to detect different CYP21A2 variants simultaneously.

AIMS

Targeted long-read sequencing method was used to detect all types of CYP21A2 variants in a series of patients with 21-OHD.

METHODS

A total of 59 patients with 21-OHD were enrolled from Peking Union Medical College Hospital. Long-range locus-specific PCR and long-read sequencing (LRS) were performed to detect the pathogenic variants in CYP21A2.

RESULTS

Copy-number variants of CYP21A2 were found in 25.4% of patients, including 5.1% with 3 copies of CYP21A2, 16.9% with 1 copy of CYP21A2, and 3.4% with 0 copy of CYP21A2. The remaining 74.6% of patients had 2 copies of CYP21A2. Pathogenic variants were identified in all 121 alleles of 59 patients. Specifically, single-nucleotide variants and small insertions/deletions (< 50 bp) were detected in 79 alleles, of which conversed from CYP21A1P were detected in 63 alleles, and rare variants were found in the other 16 alleles. Large gene conversions (> 50 bp) from pseudogene were detected in 10 alleles, and different chimeric genes (CYP21A1P/CYP21A2 or TNXA/TNXB) formed by large deletions were detected in 32 alleles. Of all variants, p.I173N was the most common variant (19.0%).

CONCLUSIONS

Our study demonstrated that targeted long-read sequencing is a comprehensive method for detecting CYP21A2 variations, which is helpful for genetic diagnosis in 21-OHD patients.

Transcription factor encoding gene OsC1 regulates leaf sheath color through anthocyanidin metabolism in Oryza rufipogon and Oryza sativa

Carbohydrates, proteins, lipids, minerals and vitamins are nutrient substances commonly seen in rice grains, but anthocyanidin, with benefit for plant growth and animal health, exists mainly in the common wild rice but hardly in the cultivated rice. To screen the rice germplasm with high intensity of anthocyanidins and identify the variations, we used metabolomics technique and detected significant different accumulation of anthocyanidins in common wild rice (Oryza rufipogon, with purple leaf sheath) and cultivated rice (Oryza sativa, with green leaf sheath). In this study, we identified and characterized a well-known MYB transcription factor, OsC1, through phenotypic (leaf sheath color) and metabolic (metabolite profiling) genome-wide association studies (pGWAS and mGWAS) in 160 common wild rice (O. rufipogon) and 151 cultivated (O. sativa) rice varieties. Transgenic experiments demonstrated that biosynthesis and accumulation of cyanidin-3-Galc, cyanidin 3-O-rutinoside and cyanidin O-syringic acid, as well as purple pigmentation in leaf sheath were regulated by OsC1. A total of 25 sequence variations of OsC1 constructed 16 functional haplotypes (higher accumulation of the three anthocyanidin types within purple leaf sheath) and 9 non-functional haplotypes (less accumulation of anthocyanidins within green leaf sheath). Three haplotypes of OsC1 were newly identified in our germplasm, which have potential values in functional genomics and molecular breeding of rice. Gene-to-metabolite analysis by mGWAS and pGWAS provides a useful and efficient tool for functional gene identification and omics-based crop genetic improvement.

MKK3 Cascade Regulates Seed Dormancy Through a Negative Feedback Loop Modulating ABA Signal in Rice

BACKGROUND

With the increasing frequency of climatic anomalies, high temperatures and long-term rain often occur during the rice-harvesting period, especially for early rice crops in tropical and subtropical regions. Seed dormancy directly affects the resistance to pre-harvest sprouting (PHS). Therefore, in order to increase rice production, it is critical to enhance seed dormancy and avoid yield losses to PHS. The elucidation and utilization of the seed dormancy regulation mechanism is of great significance to rice production. Preliminary results indicated that the OsMKKK62-OsMKK3-OsMPK7/14 module might regulate ABA sensitivity and then control seed dormancy. The detailed mechanism is still unclear.

RESULTS

The overexpression of OsMKK3 resulted in serious PHS. The expression levels of OsMKK3 and OsMPK7 were upregulated by ABA and GA at germination stage. OsMKK3 and OsMPK7 are both located in the nucleus and cytoplasm. The dormancy level of double knockout mutant mkk3/mft2 was lower than that of mkk3, indicating that OsMFT2 functions in the downstream of MKK3 cascade in regulating rice seeds germination. Biochemical results showed that OsMPK7 interacted with multiple core ABA signaling components according to yeast two-hybrid screening and luciferase complementation experiments, suggesting that MKK3 cascade regulates ABA signaling by modulating the core ABA signaling components. Moreover, the ABA response and ABA responsive genes of mpk7/14 were significantly higher than those of wild-type ZH11 when subjected to ABA treatment.

CONCLUSION

MKK3 cascade mediates the negative feedback loop of ABA signal through the interaction between OsMPK7 and core ABA signaling components in rice.

Risk factors for portal vein system thrombosis after partial splenic embolisation in cirrhotic patients with hypersplenism

AIM

To determine risk factors for portal venous system thrombosis (PVST) after partial splenic artery embolisation (PSAE) in cirrhotic patients with hypersplenism.

MATERIALS AND METHODS

Between March 2014 and February 2022, 428 cirrhotic patients with hypersplenism underwent partial splenic artery embolisation and from these patients 208 were enrolled and 220 were excluded. Medical records of enrolled patients were collected. Computed tomography (CT) images were reviewed by two blinded, independent radiologists. Statistical analyses were performed by using SPSS.

RESULTS

Progressive PVST was observed in 18.75% (39/208) of cirrhotic patients after PSAE. No significant differences in peripheral blood counts, liver function biomarkers, and renal function were observed between the patients with progressive PVST and the patients without progressive PVST. The imaging data showed significant differences in PVST, the diameters of the portal, splenic, and superior mesenteric veins between the progressive PVST group and non-progressive PVST group. Univariate and multivariate analysis demonstrated portal vein thrombosis, spleen infarction percentage, and the diameter of the splenic vein were independent risk factors for progressive PVST. Seventeen of 173 (9.83%) patients showed new PVST; the growth of PVST was observed in 62.86% (22/35) of the patients with pre-existing PVST. Spleen infarction percentage and the diameter of the splenic vein were independent risk factors for new PVST after PSAE.

CONCLUSION

The present study demonstrated portal vein thrombosis, spleen infarction percentage, and the diameter of the splenic vein were independent risk factors for PVST after PSAE in cirrhotic patients with hypersplenism.

Bridging the Gap of Radiotherapy Treatment Planning Quality between High-Income, and Low- and Middle-Income Countries Using Knowledge-Based Planning

PURPOSE/OBJECTIVE(S)

Radiotherapy departments in low- and middle-income countries (LMICs) like Guatemala have recently introduced intensity-modulated radiotherapy (IMRT). IMRT has become the standard of care in high-income countries (HIC) due to reduced toxicity and improved outcomes in some cancers. The purpose of this work is to show the feasibility of adapting knowledge-based (KB) models established in a HIC to a LMIC lacking experience in IMRT to improve plan quality and planning efficiency.

MATERIALS/METHODS

A Halcyon Linac was installed at our clinic in Guatemala in 2019 and has been used to treat approximately 90 patients daily with IMRT. A model developed on a cohort of head and neck cancer patients at a US academic radiotherapy center were applied at our center to create 20head and neck VMAT plans with different prescriptions, including simultaneous-integrated and sequential boosts.

RESULTS

The plans created using the KB models achieved similar coverage of the planning target volume for each plan KB plans showed better 1) Parotid sparing with a mean dose reduction between 5%-25% and spinal cord maximum dose reduction between 3%-15%. The time efficiency to create VMAT plans using KB model versus manual planning improved four-fold, on average one hour versus more than 4 hours, respectively.

CONCLUSION

Despite different prescriptions, guidelines and demographics of cancer patients between two institutions in a HIC and LMIC, this work demonstrates that KB planning can be used to generate better and more consistent VMAT plans versus manually created plans. In addition, KB planning has the potential to greatly increase planning efficiency higher efficiency and help address the shortage of medical physicists and dosimetrists in LMICs.

Dissecting Systemic T Cell Responses after Stereotactic Ablative Radiotherapy in NSCLC by Single-Cell RNA and T Cell Receptor Sequencing

PURPOSE/OBJECTIVE(S)

There is accumulating evidence that stereotactic ablative radiotherapy (SABR) modulates immune responses to cancer; combining SABR and immunotherapy could promote the abscopal effect, but the precise effects of SABR on patients' systemic T cells is unclear. Here, we investigated SABR-induced systemic T cell response in early-stage non-small cell lung cancer (NSCLC) by single-cell RNA and T cell receptor sequencing.

MATERIALS/METHODS

We performed single-cell RNA and T cell receptor sequencing on 29,439 T cells from four pairs of peripheral blood before and after SABR in early-stage NSCLC patients. Cell clustering and dimensionality reduction, SingleR, feature genes score, and TCR profiling analyses were used to investigate the heterogeneity of T cells and their changes following SABR.

RESULTS

We identified fourteen T cell subtypes using unsupervised graph-based clustering of uniform manifold approximation and projection. By comparing the gene set scores of CD8_TE and CD8_EM pre- and post-SABR, we found both cytotoxic and inhibitory scores were significantly elevated in CD8_TE (both P < 0.001), while cytotoxic score was significantly increased in CD8_EM (P < 0.001) after SABR. We also found that CD4_TE showed increased cytotoxic scores and decreased Treg scores (P < 0.001 and < 0.05, respectively), while Treg cells showed decreased inhibitory and Treg scores (P < 0.001 and <0.01, respectively) after SABR. The proportion of large TCR clones was higher after SABR, which was accompanied by a decrease in proportion of single clones. When we compared the transcriptomes of CD8_TE cells between the single, small and large clones post-SABR, we found high expression of GZMB and KLRC3 in cells with large clones, and GZMK, IL7R, and SELL in small and single clones. This suggested that T cells after SABR with large clones may have higher cytotoxicity than those with small and single clones.

CONCLUSION

Our study identified systemic T cell activation after SABR at single-cell resolution, providing unprecedented insight into the immune-modulatory role of SABR in early-stage NSCLC.

Standardizing LT Chest Wall Radiotherapy Treatment Planning in a Low- or Middle- Income Country Radiotherapy Clinic Using Knowledge Based Planning

PURPOSE/OBJECTIVE(S)

Radiotherapy departments in low- or middle-income countries (LMICs) tend to lag behind introducing emerging technologies like intensity-modulated radiotherapy (IMRT). IMRT has become the standard of care in high-income countries (HIC) due to reduced toxicity and improved outcomes in a wide variety of cancers. The purpose of this work is showing the results of left Chest-Wall knowledge-based planning (KBP) standardization and implementation in a LMIC setting.

MATERIALS/METHODS

A Halcyon Linac was installed at our clinic in Guatemala in 2019 and currently used to treat ∼90 IMRT patients daily. The standardization of IMRT procedures has been difficult for complex sites like chest-wall. The steps for standardization included: AAPM TG-263 nomenclature implementation, and planning workflows within the TPS, creation of optimization structures, and plan quality evaluation following RTOG1005 protocol hypofractionation arm. 25 plans were created manually achieving all RTOG1005 protocol constraints. The statistics were analyzed trough the model analytics tool provided by KPB manufacturer.

RESULTS

The results show that more plans are needed to improve the KBP model. This initial model was used to create a standardized clinical protocol in the TPS in order to continue adding plans to the KBP model database. This approach ensures that we obtain consistent plan quality and standardize our planning. The manual planning objectives achieved: CONCLUSION: The experience using the TPS to standardize our treatment planning process achieved good consistency in our planning objectives. This approach will help create KBP models according to our own clinic-specific requirements. Future work will be made to compare our LMIC KBP models with those made at a HIC academic radiotherapy center.

Impact of AI-Based Auto-Segmentation on Radiotherapy Processes in Low and Middle-Income Countries

PURPOSE/OBJECTIVE(S)

Radiotherapy processes require significant human resources and expertise, creating a barrier for rapid deployment in low and middle-income countries (LMICs). Optimal radiotherapy (RT) relies on accurate segmentation of tumor targets and organs-at-risk (OARs) during the RT planning process. This study reports the impact of AI-based auto-segmentation on RT processes in an LMIC.

MATERIALS/METHODS

Ten patients including five head and neck (HN), and five prostate cancer patients were randomly selected. Their planning CT images were subjected to auto- segmentation using an FDA-approved AI software tool, and manual segmentation by an experienced radiation oncologist from a Sub-Saharan African RT clinic. The control data consisted of contours from an experienced radiation oncologist and dosimetrists at a large academic institution in the US. For prostate cases, the contours included the prostate, seminal vesicles, bladder, rectum, penile bulb, and both femoral heads. For HN cases, the contours included the brain, brainstem, bilateral eyes, lens, optic nerves, cochlea, parotids, optic chiasm, spinal cord, oral cavity, and mandible. The time to complete the segmentation was recorded for both auto-segmentation and manual contours from the LMIC. The DICE similarity coefficients were used for comparative evaluation.

RESULTS

The average time for contouring per patient was 2 minutes for AI compared to 57 minutes for manual contouring in the LMIC. When comparing the control data, AI pelvic contours provide a slightly better agreement than LMIC manual contours for all the OARs, with the following mean DICE coefficients for AI vs LMIC manual contours: bladder (0.971 vs 0.958), left femoral head (0.960 vs 0.949), right femoral head (0.959 vs 0.941), rectum (0.880 vs 0.867), prostate (0.836 vs 0.824), seminal vesicles (0.696 vs 0.580), and penile bulb (0.536 vs 0.528). For HN contours, AI provide a better agreement for 7 of 11 OARs than the LMIC manual contours, with the following mean DICE coefficients: brain (0.972 vs 0.982), mandible (0.877 vs 0.925), right parotid (0.847 vs 0.800), left parotid (0.798 vs 0.792), spinal cord (0.837 vs 0.821), left eye (0.875 vs 0.832), right eye (0.867 vs 0.836), brainstem (0.866 vs 852), oral cavity (0.796 vs 0.787), left lens (0.650 vs 0.729) and right lens (0.671 vs 0.682). Neither AI contours nor LMIC manual contours had good agreement with the control data (<0.600) for optic nerves, chiasm, and cochlea due to their small volumes.

CONCLUSION

AI-based auto-segmentation tools are capable of producing contours of comparable quality to those generated by manual segmentation for both pelvic and HN cancer patients in LMICs, while also resulting in substantial time savings. AI-based auto-segmentation holds tremendous potential for improving radiotherapy care in LMICs with limited sources.

Improvement of Rice Blast Resistance in TGMS Line HD9802S through Optimized Anther Culture and Molecular Marker-Assisted Selection

Rice blast caused by Magnaporthe oryzae is one of the most serious rice diseases worldwide. The early indica rice thermosensitive genic male sterile (TGMS) line HD9802S has the characteristics of stable fertility, reproducibility, a high outcrossing rate, excellent rice quality, and strong combining ability. However, this line exhibits poor blast resistance and is highly susceptible to leaf and neck blasts. In this study, backcross introduction, molecular marker-assisted selection, gene chipping, anther culture, and resistance identification in the field were used to introduce the broad-spectrum blast-resistance gene R6 into HD9802S to improve its rice blast resistance. Six induction media were prepared by varying the content of each component in the culture medium. Murashige and Skoog's medium with 3 mg/L 2,4-dichlorophenoxyacetic acid, 2 mg/L 1-naphthaleneacetic acid, and 1 mg/L kinetin and N6 medium with 800 mg/L casein hydrolysate, 600 mg/L proline, and 500 mg/L glutamine could improve the callus induction rate and have a higher green seedling rate and a lower white seedling rate. Compared to HD9802S, two doubled haploid lines containing R6 with stable fertility showed significantly enhanced resistance to rice blast and no significant difference in spikelet number per panicle, 1000-grain weight, or grain shape. Our findings highlight a rapid and effective method for improving rice blast resistance in TGMS lines.

[Evolution and progress of surgical intervention strategies for acute pancreatitis]

Acute pancreatitis is one of the common surgical acute abdominal diseases. Since people first recognized acute pancreatitis in the middle of the nineteenth century, a diversified minimally invasive treatment model with standardization has been formed today. According to the main line of surgical intervention of acute pancreatitis treatment,this period can be roughly divided into five stages:exploration stage, conservative treatment stage, pancreatectomy stage, debridement and drainage of the pancreatic necrotic tissue stage, and minimally invasive treatment as the first choice led by the multidisciplinary team mode stage. Throughout history, the evolution and progress of surgical intervention strategies for acute pancreatitis cannot be separated from the progress of science and technology, the update of treatment concepts and the further understanding of the pathogenesis. This article will summarize the surgical characteristics of acute pancreatitis treatment at each stage to explain the development of surgical treatment of acute pancreatitis,to help investigate the development of surgical treatment of acute pancreatitis in the future.

[Application of veno-arterio-venous extracorporeal membrane oxygenation in patients with critical respiratory failure combined with refractory shock]

Objective: To preliminarily analyze the application experience of veno-arterio-venous extracorporeal membrane oxygenation (VAV-ECMO).The VAV-ECMO is a rescue strategy for patients with extremely critical respiratory failure combined with refractory shock. Methods: From February 2016 to February 2022, the characteristics and outcomes of patients who were started on either veno-venous or veno-arterial ECMO due to respiratory or hemodynamic failure, and then converted to VAV-ECMO in respiratory intensive care unit (ICU) of Beijing Chaoyang Hospital were analyzed. Results: A total of 15 patients underwent VAV-ECMO, aged 53 (40, 65) years, and 11 of whom were male. Within the group, VV-ECMO was initially used in 12 patients due to respiratory failure, but then VAV-ECMO was used due to cardiogenic shock (7/12) and septic shock (4/12), while VAV-ECMO was established in two patients due to lung transplantation. One patient was diagnosed with pneumonia complicated by septic shock, which was initially determined to be VA-ECMO, but then switched to VAV-ECMO because it was difficult to maintain oxygenation. The time from the establishment of VV or VA-ECMO to the switch to VAV-ECMO was 3 (1, 5) days and the VAV-ECMO support time was 5 (2, 8) days. ECMO-related complications were bleeding, mostly in the digestive tract (n=4) and airway hemorrhage (n=4), without intracranial hemorrhage, and poor arterial perfusion of the lower limbs (n=2). Among these 15 patients, the overall ICU mortality was 53.3%. The mortality of patients who received VAV-ECMO due to septic shock and cardiogenic shock was 100% (4/4) and 42.8% (3/7), respectively. Two patients who received VAV-ECMO due to lung transplantation all survived. Conclusion: VAV-ECMO may be a safe and effective treatment for carefully selected patients with critical respiratory failure associated with cardiogenic shock or end-stage lung disease lung transplantation transition, however, patients with septic shock may benefit the least.

[The mechanism, inducement and long-term effects of acquired weakness in intensive care units]

With the development of critical care medicine, the case fatality rate in intensive care units (ICU) patients has decreased significantly, but most patients still suffer from the long-term problems of related complications after discharge, which seriously affects the quality of life and social integration after discharge. Complications such as ICU acquired weakness (ICU-AW) and Post-ICU Syndrome (PICS) are not uncommon throughout the treatment of severe patients. The treatment of critically ill patients should not only focus on the treatment of the disease, but also gradually extend to the whole-process physiological-psychological-social medical intervention mode in the ICU, during the stay in the general ward and after discharge. On the basis of ensuring patient safety, patients' physical and psychological status assessment in the early stage of ICU admission, and disease prevention as soon as possible, which can reduce the long-term impact on the quality of life and social work after discharge.

OsGLP3-7 positively regulates rice immune response by activating hydrogen peroxide, jasmonic acid, and phytoalexin metabolic pathways

Although germin-like proteins (GLPs) have been demonstrated to participate in plant biotic stress responses, their specific functions in rice disease resistance are still largely unknown. Here, we report the identification and characterization of OsGLP3-7, a member of the GLP family in rice. Expression of OsGLP3-7 was significantly induced by pathogen infection, jasmonic acid (JA) treatment, and hydrogen peroxide (H₂ O₂ ) treatment. OsGLP3-7 was highly expressed in leaves and sublocalized in the cytoplasm. Overexpression of OsGLP3-7 increased plant resistance to leaf blast, panicle blast, and bacterial blight, whereas disease resistance in OsGLP3-7 RNAi silenced plants was remarkably compromised, suggesting this gene is a positive regulator of disease resistance in rice. Further analysis showed that OsGLP3-7 has superoxide dismutase (SOD) activity and can influence the accumulation of H₂ O₂ in transgenic plants. Many genes involved in JA and phytoalexin biosynthesis were strongly induced, accompanied with elevated levels of JA and phytoalexins in OsGLP3-7-overexpressing plants, while expression of these genes was significantly suppressed and the levels of JA and phytoalexins were reduced in OsGLP3-7 RNAi plants compared with control plants, both before and after pathogen inoculation. Moreover, we showed that OsGLP3-7-dependent phytoalexin accumulation may, at least partially, be attributed to the elevated JA levels observed after pathogen infection. Taken together, our results indicate that OsGLP3-7 positively regulates rice disease resistance by activating JA and phytoalexin metabolic pathways, thus providing novel insights into the disease resistance mechanisms conferred by GLPs in rice.

Semiparametric Efficient G-estimation with Invalid Instrumental Variables

The instrumental variable method is widely used in the health and social sciences for identification and estimation of causal effects in the presence of potential unmeasured confounding. In order to improve efficiency, multiple instruments are routinely used, leading to concerns about bias due to possible violation of the instrumental variable assumptions. To address this concern, we introduce a new class of G-estimators that are guaranteed to remain consistent and asymptotically normal for the causal effect of interest provided that a set of at least γ out of K candidate instruments are valid, for γ≤K set by the analyst ex ante, without necessarily knowing the identity of the valid and invalid instruments. We provide formal semiparametric efficiency theory supporting our results. Both simulation studies and applications to the UK Biobank data demonstrate the superior empirical performance of our estimators compared to competing methods.

The genetic basis of grain protein content in rice by genome-wide association analysis

The grain protein content (GPC) of rice is an important factor that determines its nutritional, cooking, and eating qualities. To date, although a number of genes affecting GPC have been identified in rice, most of them have been cloned using mutants, and only a few genes have been cloned in the natural population. In this study, 135 significant loci were detected in a genome-wide association study (GWAS), many of which could be repeatedly detected across different years and populations. Four minor quantitative trait loci affecting rice GPC at four significant association loci, qPC2.1, qPC7.1, qPC7.2, and qPC1.1, were further identified and validated in near-isogenic line F2 populations (NIL-F2), explaining 9.82, 43.4, 29.2, and 13.6% of the phenotypic variation, respectively. The role of the associated flo5 was evaluated with knockdown mutants, which exhibited both increased grain chalkiness rate and GPC. Three candidate genes in a significant association locus region were analyzed using haplotype and expression profiles. The findings of this study will help elucidate the genetic regulatory network of protein synthesis and accumulation in rice through cloning of GPC genes and provide new insights on dominant alleles for marker-assisted selection in the genetic improvement of rice grain quality.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01347-z.

Creation and gene expression analysis of a giant embryo rice mutant with high GABA content

Gamma-amino butyric acid (GABA) is a natural non-protein amino acid involved in stress, signal transmission, carbon and nitrogen balance, and other physiological processes in plants. In the human body, GABA has the effects of lowering blood pressure, anti-aging, and activating the liver and kidneys. However, there are few studies on the molecular regulation mechanism of genes in the metabolic pathways of GABA during grain development of giant embryo rice with high GABA content. In this study, three glant embryo (ge) mutants of different embryo sizes were obtained by CRISPR/Cas9 knockout, and it was found that GABA, protein, crude fat, and various mineral contents of the ge mutants were significantly increased. RNA-seq and qRT-PCR analysis showed that in the GABA shunt and polyamine degradation pathways, the expression levels of most of the genes encoding enzymes promoting GABA accumulation were significantly upregulated in the ge-1 mutant, whereas, the expression levels of most of the genes encoding enzymes involved GABA degradation were significantly downregulated in the ge-1 mutant. This is most likely responsible for the significant increase in GABA content of the ge mutant. These results help reveal the molecular regulatory network of GABA metabolism in giant embryo rice and provide a theoretical basis for the study of its development mechanisms, which is conducive to the rapid cultivation of GABA-rich rice varieties, promoting human nutrition, and ensuring health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01353-1.

[Clinical characteristics and outcomes of acute respiratory distress syndrome caused by severe Chlamydia psittaci pneumonia]

Objective: To investigate the clinical characteristics and outcomes of acute respiratory distress syndrome (ARDS) caused by Chlamydia psittaci pneumonia. Methods: From June 2016 to January 2021, 10 cases were diagnosed as severe Chlamydia psittaci pneumonia induced ARDS in Intensive Care Unit of Respiratory and Critical Care Medicine Department (RICU) of Beijing Chao-Yang Hospital Affiliated to Capital Medical University. We collected the clinical data including clinical features, laboratory tests, imaging and outcomes of the patients. Results: The pathogenic diagnosis was confirmed by metagenomic Next-generation Sequencing (mNGS) in these 10 patients, with a median age of 59 (46, 67) years. In addition to high fever, cough and dyspnea, the patients also had multiple organ involvement. Six patients had elevated peripheral leukocyte count, 10 cases had increased type B natriuretic peptide, 7 cases had increased aspartate aminotransferase/alanine aminotransferase, 9 cases had hyponatremia and 3 cases had elevated creatinine. The imaging findings were bilateral consolidation with air bronchogram and infiltrates, and pleural effusion were found in 5 cases. All cases were combined with respiratory failure. Six patients received invasive mechanical ventilation. Nine patients received moxifloxacin and one patient was administrated with Azithromycin. All the patients were improved and discharged after the treatment, and the mean duration of RICU stay was 13.5 (11, 16.7) days. One month follow-up of nine patients showed significant improvement in lung lesions. Conclusions: Severe Chlamydia psittiaci pneumonia may be complicated with respiratory failure and/or multiple organ involvement. For severe pneumonia with an exposure history of sick birds, the possibility of Chlamydia psittaci infection should be considered. mNGS may help etiological diagnosis. All patients in this study had a good prognosis after targeted treatment.

Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection

Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for conserving natural genetic diversity and providing novel traits for rice breeding. In the present study, we developed 1,592 SNPs by multiplex PCR and next-generation sequencing (NGS) technology and used them to genotype 998 O. rufipogon accessions from 14 agroclimatic zones in Guangdong and Hainan Provinces, China. These SNPs were mapped onto 12 chromosomes, and the average MAF value was 0.128 with a minimum of 0.01 and a maximum of 0.499. The O. rufipogon accessions were classified into ten groups. The mean Nei's diversity index and Shannon-Wiener index (I) were 0.187 and 0.308, respectively, in all populations, indicating that O. rufipogon accessions had rich genetic diversity. There were also differences in the genetic diversity of O. rufipogon resources in the 14 regions. Hainan populations possessed higher levels of genetic diversity, whereas the Guangzhou population had lower levels of genetic diversity than did the other populations. Phylogenetic analysis revealed that the genetic relationship among the distribution sites of O. rufipogon was closely related to geographical location. Based on genetic distance, a core collection of 299 accessions captured more than 99% of the genetic variation in the germplasm. This study provides insights into O. rufipogon conservation, and the constructed core collection provides valuable resources for future research and genomics-assisted breeding of rice.

Vented Individual Patient (VIP) Hoods for the Control of Infectious Airborne Diseases in Healthcare Facilities

By providing a means of separating the airborne emissions of patients from the air breathed by healthcare workers (HCWs), vented individual patient (VIP) hoods, a form of local exhaust ventilation (LEV), offer a new approach to reduce hospital-acquired infection (HAI). Results from recent studies have demonstrated that, for typical patient-emitted aerosols, VIP hoods provide protection at least equivalent to that of an N95 mask. Unlike a mask, hood performance can be easily monitored and HCWs can be alerted to failure by alarms. The appropriate use of these relatively simple devices could both reduce the reliance on personal protective equipment (PPE) for infection control and provide a low-cost and energy-efficient form of protection for hospitals and clinics. Although the development and deployment of VIP hoods has been accelerated by the coronavirus disease 2019 (COVID-19) pandemic, these devices are currently an immature technology. In this review, we describe the state of the art of VIP hoods and identify aspects in need of further development, both in terms of device design and the protocols associated with their use. The broader concept of individual patient hoods has the potential to be expanded beyond ventilation to the provision of clean conditions for individual patients and personalized control over other environmental factors such as temperature and humidity.

[Novel MFN2, BSCL2 and LRSAM1 variants in a cohort of Chinese patients with Charcot-Marie-Tooth disease]

Objective: Charcot-Marie-Tooth disease (CMT) comprises a group of clinically and genetically heterogeneous inherited neuropathies with an estimated prevalence of 1 in 2500. This study aimed to analyze the clinical and mutational characteristics of Chinese CMT patients with MFN2, BSCL2 and LRSAM1 variants. Methods: In this study, genetic analysis was performed in 206 Chinese patients at Chinese PLA General Hospital from December 2012 to March 2020 with clinical diagnosis of CMT, and reported variants of MFN2, BSCL2 and LRSAM1 related to CMT2. Results: We reported ten MFN2 mutations in ten unrelated patients (7 male, 3 female), two of whom had positive family history. Three novel mutations were detected including c.475-2A>G (splicing); c.687dupA (p.E230Rfs*16) and c.558dupT (p.S186fs). We reported three BSCL2 mutations of four unrelated patients, including c.461C>G (p.S154W), c.461C>T(p.S154L), and novel variants of c.1309G>C (p.A437P) and c.845C>T (p.A282V). Furthermore, two novel variants of LRSAM1, including c.1930G>T (p.G644C) and c.1178T>A (p.L393Q) were detected in two unrelated patients. Conclusion: Mutational spectrum of MFN2-, BSCL2-and LRSAM1-related CMT disease is expanded with the identification of novel variants in Chinese patients.

[Analysis of China's influenza vaccine application policy based on the macro model of the health system]

This article uses the analysis framework of the macro model of the health system to analyze the influenza vaccine policy documents issued by the state and governments at all levels from three perspectives: structure, process and results, and provides a scientific basis for improving the application strategy of influenza vaccine. It is suggested that on the basis of continuing to strengthen publicity, mobilization and organizational guarantee, measures to promote the application of influenza vaccine in China by exploring multi-channel financing mechanisms, combining the experience of new crown vaccination to improve the convenience of influenza vaccination, and scientifically setting vaccination rate targets, improve preparedness for an influenza pandemic.

[Weaning of veno-venous extracorporeal membrane oxygenation: when to use the "resting lung"]

Differences in weaning strategies for veno-venous extracorporeal membrane oxygenation (VV-ECMO) are based on expert opinions rather than clinical evidence. Therefore, each center has its own "unique skills". The timing of VV-ECMO weaning has not received due attention. It is difficult to find research on the choice of VV-ECMO weaning timing in the database. There are few studies involving VV-ECMO that describe the weaning process in detail. At present, the weaning process of VV-ECMO is mainly based on expert opinions. This article classified the current VV-ECMO weaning strategies, appealed to a unified VV-ECMO weaning protocol in China as soon as possible, and further improved the prognosis of patients with extracorporeal life support.

[Treatment choices for infected pancreatic necrosis:surgery debridement or endoscopy drainage?]

Infected pancreatic necrosis (IPN) is a crucial reason for the poor prognosis of patients with acute pancreatitis,which is complicated and difficult to predict the outcomes. Surgery is an important way to cure IPN,and "step-up approach" is the mainstream mode of IPN treatment. In the era of minimally invasive surgery,the full course endoscopic treatment of IPN has been gradually hot and achieved good outcomes as endoscopic technology' improvement. However,it is controversial that whether technique is better for IPN by surgery debridement or endoscopy drainage,and there is no consensus on the scope of applicability and the timing of intervention. The paper aims to explore the intervention methods,indications and timing of endoscopic and surgical treatment of IPN and elaborate the selection strategies of them in clinical practice,so as to develop individualized treatment options,accurately implement minimally invasive intervention and improve the prognosis.

[SWOT analysis of influenza vaccination promotion of primary care staff based on the perspective of the supplier, customer, and management]

Objective: To analyze the situation of influenza vaccination among primary healthcare workers, find out the problems, and explore the strategies and measures to promote influenza vaccination among grass-roots medical staff. Methods: From April to May 2021, key insider interviews and literature research were carried out based on the perspectives of influenza vaccine suppliers (influenza vaccine manufacturers), consumers (primary medical institutions and primary healthcare workers), and managers (governments at all levels, health administrative departments and disease prevention and control departments). The SWOT (strengths, weaknesses, opportunities, and threats) analysis technique was used to comprehensively evaluate the current situation of influenza vaccination among grass-roots healthcare workers, and a SWOT analysis matrix was established. Results: Influenza vaccination of grass-roots healthcare workers have advantages and opportunities, including primary medical and health institutions' vital influenza vaccination accessibility, influenza vaccine safety is higher, COVID-19 outbreak improves the public awareness of respiratory infectious diseases and vaccine production enthusiasm, coronavirus vaccination has strengthened the capacity of the vaccine distribution system. There are also disadvantages and threats such as the high price of influenza vaccine, insufficient supply, low awareness of influenza vaccine vaccination among grass-roots healthcare workers, lack of demand assessment mechanism on influenza vaccine, poor vaccine deployment, structural imbalance in vaccine supply in different areas, and severe vaccine waste. SWOT analysis matrix of the influenza vaccination status of grass-roots healthcare workers was established, forming dominant opportunity (SO) strategy, dominant threat (ST) strategy, inferior opportunity (WO) strategy, and inferior threat (WT) strategy. Conclusion: Measures should be taken by the supplier, the demand-side, and the management side to improve the influenza vaccine coverage rate of primary healthcare workers, but the emphasis should be on the coordination and management of the management side.

MiR-572 promotes the development of non-small cell lung cancer by targeting KLF2

OBJECTIVE

The aim of this study was to uncover the role of miR-572 in regulating proliferative and migratory abilities in non-small cell lung cancer (NSCLC) and the possible mechanism.

PATIENTS AND METHODS

Expression levels of miR-572 in 46 matched NSCLC and paracancerous samples were detected. The relationship between miR-572 level and clinical features of NSCLC was analyzed. Subsequently, the regulatory effects of miR-572 on proliferative and migratory abilities in lung cancer cells were assessed by functional experiments. Finally, the downstream genes of miR-572 were tested by luciferase assay, and their functions in the development of NSCLC were finally explored by rescue experiments.

RESULTS

It was found that miR-572 was upregulated in NSCLC samples. High level of miR-572 predicted high rates of lymphatic and distant metastases, as well as poor prognosis in NSCLC. Besides, the knockdown of miR-572 suppressed proliferative and migratory abilities in A549 and SPC-A1 cells. KLF2 was identified to be the downstream gene of miR-572, which was involved in the regulation of NSCLC phenotypes influenced by miR-572.

CONCLUSIONS

MiR-572 is closely linked to metastasis and prognosis in NSCLC patients, and it promotes the malignant development of NSCLC via targeting KLF2.

Hyperspectral Imaging during Normothermic Machine Perfusion—A Functional Classification of Ex Vivo Kidneys Based on Convolutional Neural Networks

Facing an ongoing organ shortage in transplant medicine, strategies to increase the use of organs from marginal donors by objective organ assessment are being fostered. In this context, normothermic machine perfusion provides a platform for ex vivo organ evaluation during preservation. Consequently, analytical tools are emerging to determine organ quality. In this study, hyperspectral imaging (HSI) in the wavelength range of 550–995 nm was applied. Classification of 26 kidneys based on HSI was established using KidneyResNet, a convolutional neural network (CNN) based on the ResNet-18 architecture, to predict inulin clearance behavior. HSI preprocessing steps were implemented, including automated region of interest (ROI) selection, before executing the KidneyResNet algorithm. Training parameters and augmentation methods were investigated concerning their influence on the prediction. When classifying individual ROIs, the optimized KidneyResNet model achieved 84% and 62% accuracy in the validation and test set, respectively. With a majority decision on all ROIs of a kidney, the accuracy increased to 96% (validation set) and 100% (test set). These results demonstrate the feasibility of HSI in combination with KidneyResNet for non-invasive prediction of ex vivo kidney function. This knowledge of preoperative renal quality may support the organ acceptance decision.

[Clinicopathological features of verrucous hemangioma]

Objective: To investigate the clinicopathological features, and differential diagnosis of verrucous hemangioma (VH). Methods: Twenty-eight VH cases diagnosed from 2005 to 2020 in Henan Provincial People's Hospital, Zhengzhou, China were analyzed retrospectively. Immunohistochemical studies were used to detect diagnostic markers. The mutation status of PIK3CA (exons 9 and 20) was detected using fluorescence PCR. Results: There were 13 males and 15 females in 28 cases, with the male to female ratio of 1.0∶1.2. There were 25 patients under the age of 18 years. The age range was from 10 months to 56 years (mean, 9.7 years; median, 4.5 years). There were 17 cases occurred in the lower extremities, 7 in the upper extremities and 4 in the trunk. All 28 cases were irregular red patches on the skin, which grew slowly. Some of them were thickened with uneven surface, which was light pink or red-white. Skin lesions of the 7 cases ranged from dark red and reddish brown, with a rough and hard surface. Satellite foci were present. Microscopically, 28 cases had a wide range of pathological features. Dilated, malformed vessels were observed from dermal papilla to deep soft tissue. Among them, the dermal papillary layer was mainly composed of many proliferating and expanding thin-walled capillaries and cavernous blood vessels. Thin-walled small vessels were found in the dermal reticular layer and subcutaneous fascia layer, with no obvious endothelial cell proliferation, occasional papillary hyperplasia, and lobular distribution of the malformed vessels in the fascia layer mixed with the fibroadipose tissue. There was epidermal papillary hyperplasia with hyperkeratosis and parakeratosis, lengthening and mutual fusion of epithelial horns. Immunohistochemistry showed that CD31, CD34, ERG and WT-1 were diffusely and strongly positive. The expression of GLUT-1 was present in superficial dermal vascular endothelial cells, but undetectable in the deep layer. The PIK3CA tests of 13 cases showed that no somatic mutations were found in exons 9 and 20. Twenty-five patients were followed up for 5 months to 10 years. Seven patients underwent multiple surgical resections and plastic surgeries due to the large size, and 8 patients had recurrence. Conclusions: VH is a rare congenital vascular malformation and more commonly occurs in infants and children. It tends to appear in limbs, especially lower limbs and distal limbs. Its morphology and immunophenotype are characteristic and should be distinguished from other vascular malformations and the resolution phase of infant hemangiomas. In about one third of the cases, postoperative recurrence may occur and long-term follow-up is often required.

Modified anterior midline approach to treat hyperextension bicondylar tibial plateau fractures: Surgical technique and clinical experience with 18 cases

BACKGROUND

We evaluated the modified anterior midline approach and its efficacy for hyperextension bicondylar tibial plateau (HEBTP) fractures.

METHODS

From 2015 to 2019, 18 patients with HEBTP fractures with just little posterior cortical displacement were treated using the modified anterior midline approach. The operative protocols are fully described in this article, and the following parameters: articular step-off height (ASH), posterior tibial slope angle (pTSA), and medial tibial plateau angle (mTPA) were measured perioperatively and at the final follow-up. We also recorded the Rasmussen score and range of motion (ROM) to assess knee joint function at the final follow-up.

RESULTS

No complications, such as percutaneous nerve damage, infection, skin necrosis, and internal fixation breakage or loosening occurred perioperatively. The mean time for bony union was 13.7 weeks, and the mean preoperative ASH of the anterior cortex was 4.49 mm; this was restored to its normal height after surgery. The mean preoperative pTSA and mTPA were - 5.89° and 81.69°, respectively, compared with 3.89° and 87.91°, respectively, postoperatively. Comparing the postoperative and final follow-up radiographs, there were no significant differences in ASH, pTSA, and mTPA (P < 0.05). The average Rasmussen score was 27.2 (range, 23-29) at the final follow-up. Excellent results were achieved in 14 (77.8%) patients and good in 4 (22.2%) patients. The mean ROM in flexion was 123.2° and 2.9° in extension at the final follow-up.

CONCLUSIONS

This study suggested that the modified anterior midline approach is a reasonable alternative for HEBTP fracture repair.

[Rethinking on the classification of infected pancreatic necrosis and its surgical intervention strategy]

Infected pancreatic necrosis is a complex disease which is difficult to deal with.Timely and effective removal of the infection is the core of surgical treatment.Accurate determination and location of the infected area as well as targeted drainage and debridement are the key to further enhance the overall cure rate of necrotizing pancreatitis.Combining the clinical practice and relevant literatures,the classification of infected pancreatic necrosis is tentatively proposed based on the site of infection and necrosis or treatment in this paper.Meanwhile, the diversified intervention methods in the new era and the issues that need attention in the concept of step-up approach are rediscussed, aiming at scientific planning of treatment strategies and targeted intervention methods to reduce patients' mortality and improve prognosis.