Fine mapping and analysis of a candidate gene controlling Phytophthora blight resistance in cucumber

Cucumber blight is a destructive disease. The best way to control this disease is resistance breeding. This study focuses on disease resistance gene mapping and molecular marker development. We used the resistant cucumber, JSH, and susceptible cucumber, B80, as parents to construct F2 populations. Bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) were used, from which we developed cleaved amplified polymorphic sequence (CAPs) markers to map the resistance gene. Resistance in F2 individuals showed a segregation ratio of resistance:susceptibility close to 3:1. The gene in JSH resistant cucumber was mapped to an interval of 9.25 kb, and sequencing results for the three genes in the mapped region revealed three mutations at base sites 225, 302, and 591 in the coding region of Csa5G139130 between JSH and B80, but no mutations in coding regions of Csa5G139140 and Csa5G139150. The mutations caused changes in amino acids 75 and 101 of the protein encoded by Csa5G139130, suggesting that Csa5G139130 is the most likely resistance candidate gene. We developed a molecular marker, CAPs-4, as a closely linked marker for the cucumber blight resistance gene. This is the first report on mapping of a cucumber blight resistance gene and will provideg a useful marker for molecular breeding of cucumber resistance to Phytophthora blight.

The Effects of Heavy Metal Pollution on Soil Nitrogen Transformation and Rice Volatile Organic Compounds under Different Water Management Practices

One of the most concerning global environmental issues is the pollution of agricultural soils by heavy metals (HMs), especially cadmium, which not only affects human health through Cd-containing foods but also impacts the quality of rice. The soil's nitrification and denitrification processes, coupled with the release of volatile organic compounds by plants, raise substantial concerns. In this review, we summarize the recent literature related to the deleterious effects of Cd on both soil processes related to the N cycle and rice quality, particularly aroma, in different water management practices. Under both continuous flooding (CF) and alternate wetting and drying (AWD) conditions, cadmium has been observed to reduce both the nitrification and denitrification processes. The adverse effects are more pronounced in alternate wetting and drying (AWD) as compared to continuous flooding (CF). Similarly, the alteration in rice aroma is more significant in AWD than in CF. The precise modulation of volatile organic compounds (VOCs) by Cd remains unclear based on the available literature. Nevertheless, HM accumulation is higher in AWD conditions compared to CF, leading to a detrimental impact on volatile organic compounds (VOCs). The literature concludes that AWD practices should be avoided in Cd-contaminated fields to decrease accumulation and maintain the quality of the rice. In the future, rhizospheric engineering and plant biotechnology can be used to decrease the transport of HMs from the soil to the plant's edible parts.

Prediction of toxicity outcomes following radiotherapy using deep learning-based models: A systematic review

PURPOSE

This study aims to perform a comprehensive systematic review of deep learning (DL) models in predicting RT-induced toxicity.

MATERIALS AND METHODS

A literature review was performed following the PRISMA guidelines. Systematic searches were performed in PubMed, Scopus, Cochrane and Embase databases from the earliest record up to September 2022. Related studies on deep learning models for radiotherapy toxicity prediction were selected based on predefined PICOS criteria.

RESULTS

Fourteen studies of radiotherapy-treated patients on different types of cancer [prostate (n=2), HNC (n=4), liver (n=2), lung (n=4), cervical (n=1), and oesophagus (n=1)] were eligible for inclusion in the systematic review. Information regarding patient characteristics and model development was summarized. Several approaches, such as ensemble learning, data augmentation, and transfer learning, that were utilized by selected studies were discussed.

CONCLUSION

Deep learning techniques are able to produce a consistent performance for toxicity prediction. Future research using large and diverse datasets and standardization of the study methodologies are required to improve the consistency of the research output.

Global burden of metabolic diseases: data from Global Burden of Disease 2000-2019. A cosortium of metabolic disease

Funding Acknowledgements

Type of funding sources: None.

Background

The growing prevalence of metabolic diseases is a major concern. We sought to examine the global trends and mortality of metabolic diseases using estimates from the Global Burden of Diseases, Injuries and Risk Factors Study (GBD) 2019.

Methods

Global estimates of prevalence, deaths, and disability-adjusted life year (DALYs) from 2000-2019 were examined for metabolic diseases (type 2 diabetes mellitus [T2DM], hypertension, and nonalcoholic fatty liver disease [NAFLD]). For metabolic risk factors (hyperlipidemia and obesity), estimates were limited to mortality and DALYs. Death rates was compared across sex, World Health Organisation regions and Socio-demographic Index (SDI) quintiles. Age-standardised prevalence and death rates were presented per 100,000 population with 95% uncertainty intervals (UI).

Findings

From 2000 to 2019, prevalence rates increased for all metabolic diseases, with the most pronounced increase in high SDI countries. In 2019, the mean (95%UI) age-standardised prevalence per 100,000 population was estimated to be 15,023 (13,493-16,764) for NAFLD, 5,283 (4,864–5,720) for T2DM and 234 (171-313) for hypertension. The highest age-standardised death rates were observed in obesity (62·59 [39·92-89·13]; males, 66·55 [39·76-97·21]; females. 58·14 [38·53-81·39]), followed by hyperlipidemia (56·51 [41·83-73·62]; males, 67·33 [50·78-86·43]; females, 46·50 [32·70-62·38]), T2DM (18·49 [17·18-19·66], males, 67·33 [50·78-86·43]; females, 46·50 [32·70-62·38]), hypertension (15·16 [11·20-16·75]; males, 14·95 [10·32-16·75]; females, 15·05 [11·51-17·09]) and NAFLD (2·09 [1·61-2·60]; males, 2·38 [1·82-3·02]; females, 1·82 [1·41-2·27]). Mortality rates decreased over time in hyperlipidemia (-154%), hypertension (-52%) and NAFLD (-52%), but not in T2DM and obesity. The highest mortality for metabolic diseases was found in Eastern Mediterranean, and low to low-middle SDI countries.

Conclusion

The global prevalence of metabolic diseases has risen over the past two decades regardless of SDI. Attention is needed to address the unchanging mortality rates attributed to metabolic disease and the regional, socioeconomic, and sex disparities in mortality from metabolic disease.

Reconstructed meta-analysis of percutaneous coronary intervention versus coronary artery bypass grafting for left main disease

Background

Randomized controlled trials (RCTs) comparing percutaneous coronary intervention (PCI) with drug-eluting stents and coronary artery bypass grafting (CABG) for patients with left main coronary artery disease (LMCAD) have reported conflicting results.

Objectives

We performed a systematic review from inception to 23 May 2021 and one-stage reconstructed individual-patient data meta-analysis (IPDMA) that included 10-year mortality outcomes.

Methods

The primary outcome was 10-year all-cause mortality. Secondary outcomes included myocardial infarction (MI), stroke and unplanned revascularization at 5 years. We did IPDMA using published Kaplan-Meier curves to provide individual data points in coordinates and numbers at risk were used to increase the calibration accuracy of the reconstructed data. Shared frailty model or, when proportionality assumptions were not met, a restricted mean survival time model were fitted to compare outcomes between treatment groups.

Results

Of 583 articles retrieved, 5 RCTs were included. A total of 4595 patients from these 5 RCTs were randomly assigned to PCI (N=2297) or CABG (N=2298). The cumulative 10-year all-cause mortality after PCI and CABG was 12.0% versus 10.6% respectively (HR 1.093, 95% CI: 0.925–1.292; p=0.296). PCI conferred similar time-to-MI (RMST ratio 1.006, 95% CI: 0.992–1.021, p=0.391) and stroke (RMST ratio 1.005, 95% CI: 0.998–1.013, p=0.133) at 5 years. Unplanned revascularization was more frequent following PCI compared with CABG (HR 1.807, 95% CI: 1.524–2.144, p<0.001) at 5 years.

Conclusion

This meta-analysis using reconstructed participant-level time-to-event data showed no statistically significant difference in cumulative 10-year all-cause mortality between PCI versus CABG in the treatment of LMCAD.

Funding Acknowledgement

Type of funding sources: None.

THIRD bedside ultrasound protocol for rapid diagnosis of undifferentiated shock: a prospective observational study

INTRODUCTION

It is clinically challenging to differentiate the pathophysiological types of shock in emergency situations. Here, we evaluated the ability of a novel bedside ultrasound protocol (Tamponade/tension pneumothorax, Heart, Inferior vena cava, Respiratory system, Deep venous thrombosis/aorta dissection [THIRD]) to predict types of shock in the emergency department.

METHODS

An emergency physician performed the THIRD protocol on all patients with shock who were admitted to the emergency department. All patients were closely followed to determine their final clinical diagnoses. The kappa index, sensitivity, specificity, positive predictive value, and negative predictive value were calculated for the initial diagnostic impression provided by the THIRD protocol, compared with each patient's final diagnosis.

RESULTS

In total, 112 patients were enrolled in this study. The kappa index between initial impression and final diagnosis was 0.81 (95% confidence interval=0.73-0.89; P<0.001). For hypovolaemic, cardiogenic, distributive, and obstructive types of shock, the sensitivities of the THIRD protocol were 100%, 100%, 93%, and 100%, respectively; the sensitivity for a 'mixed' shock aetiology was 86%. The negative predictive value of the THIRD protocol for all five types of shock was ≥96%.

CONCLUSION

Initial diagnostic judgements determined using the THIRD protocol showed favourable agreement with the final diagnosis in patients who presented with undifferentiated shock. The THIRD protocol has great potential for use as a bedside approach that can guide the rapid management of undifferentiated shock in emergency settings, particularly for patients with obstructive, hypovolaemic, or cardiogenic shock.

Functional assessment of military aircrew applicants in a hypobaric chamber

Background

Aircrew are exposed to environmental pressure changes. In the Republic of Singapore Air Force (RSAF), applicants assessed to be at intermediate risk of otic barotrauma undergo a hypobaric chamber assessment [“trial of chamber” (TOC)] to functionally evaluate their suitability for military aircrew vocations.

Aims

To identify factors associated with TOC failure among applicants with otorhinolaryngological conditions.

Methods

All applicants to RSAF aircrew vocations who were assessed to be at intermediate risk of otic barotrauma over a 3-yr period were identified using the RSAF Aeromedical Centre’s electronic database. Their medical records, as well as the TOC assessment records of the subset of applicants who underwent TOC, were reviewed for demographic data, clinical findings, and TOC outcomes.

Results

Of the 483 identified applicants, 374 (77%) had abnormal otoscopic findings, 103 (21%) had rhinitis symptoms, and 6 (1%) had previous ENT surgery. 123 (25%) underwent TOC, of which 20 (16%) failed. Holding other predictor variables constant, the odds of TOC failure increased by 0.79 per unit decrease in BMI (95% CI 0.63–0.99), and the odds of TOC failure increased by 0.93 per kg decrease in body weight (95% CI 0.87–1.00). An abnormal tympanogram was not a statistically significant predictor of TOC failure (OR 1.96, 95% CI 0.59–6.42). Of the 47 applicants who passed TOC and were eventually recruited, none subsequently developed otic barotrauma (mean follow-up, 3.3 yr ± 1.5 yr).

Conclusions

Applicants with lower weight and BMI are more likely to develop otic barotrauma with environmental pressure change. Tympanometry cannot be reliably used to identify applicants who would more likely pass TOC.

Cystatin 2 leads to a worse prognosis in patients with gastric cancer

Despite the amazing progress in the treatment of gastric cancer (GC), it is still the third leading cause of cancer death in the world. This study explored the key genes that are related to the prognosis and pathogenesis of GC. Data from the cancer genome atlas (TCGA) and Oncomine were applied to evaluate the expression of cystatin 2 (CST2) in GC samples. Kaplan-Meier plotter was carried out to detect the overall survival of GC patients with different expression levels of CST2. Gene Set Enrichment Analysis (GSEA) was carried out to investigate the functions and pathways connected with CST2 expression. Quantitative real-time polymerase chain reaction (qPCR) and Western blot assays were used to assess CST2 expression. The biological properties of GC cells were assessed with the support of cell proliferation and Transwell assays. Important proteins involved in the regulation of CST2 in GC cell behaviors were evaluated by Western blot. Through analysis of the database, we found that CST2 expression was significantly upregulated in GC samples and actively related to GC patients' poor outcomes. Importantly, the analysis of GSEA showed that GST2 expression was closely connected with the proliferation and migration of cells, as well as the TGF-β1 signaling pathway. In addition, biological assays illustrated that over-expression of CST2 strengthened the activity and metastasis of GC cells. After the upregulation of CST2, the expression of cyclin D1, N-cadherin, vimentin, TGF-β1, and Smad4 increased, and E-cadherin expression decreased. Our findings revealed that over-expression of CST2 enhanced the growth, migration, and invasion of GC cells through modulating the epithelial-mesenchymal transition (EMT) and TGF-β1 signaling pathway, affording a possible biomarker for the treatment of GC.

Indeterminate pulmonary nodules are not associated with worse overall survival in Ewing Sarcoma

AIM

Lung metastases are a negative prognostic factor in Ewing sarcoma, however, the incidence and significance of sub-centimetre pulmonary nodules at diagnosis is unclear. The aims of this study were to (1): determine the incidence of indeterminate pulmonary nodules (IPNs) in patients diagnosed with Ewing sarcoma (2); establish the impact of IPNs on overall and metastasis-free survival and (3) identify patient, oncological and radiological factors that correlate with poorer prognosis in patients that present with IPNs on their staging chest CT.

MATERIALS & METHODS

Between 2008 and 2016, 173 patients with a first presentation of Ewing sarcoma of bone were retrospectively identified from an institutional database. Staging and follow-up chest CTs for all patients with IPN were reviewed by a senior radiologist. Clinical and radiologic course were examined to determine overall- and metastasis-free survival for IPN patients and to identify demographic, oncological or nodule-specific features that predict which IPN represent true lung metastases.

RESULTS

Following radiologic re-review, IPN were found in 8.7% of patients. Overall survival for IPN patients was comparable to those with a normal staging chest CT (2-year overall survival of 73.3% [95% CI 43.6-89] and 89.4% [95% CI 81.6-94], respectively; p = 0.34) and was significantly better than for patients with clear metastases (46.0% [95% CI 31.9-59]; p < 0.0001). Similarly, there was no difference in metastasis-free survival between 'No Metastases' and 'IPN' patients (p = 0.16). Lung metastases developed in 40% of IPN patients at a median 9.6 months. Reduction of nodule size on neoadjuvant chemotherapy was associated with worse overall survival in IPN patients (p = 0.0084).

CONCLUSION

IPN are not uncommon in patients diagnosed with Ewing sarcoma. In this study, we were unable to detect a difference in overall- or metastasis-free survival between patients with IPN at diagnosis and patients with normal staging chest CTs.

Heat and Work Along Individual Trajectories of a Quantum Bit

We use a near quantum limited detector to experimentally track individual quantum state trajectories of a driven qubit formed by the hybridization of a waveguide cavity and a transmon circuit. For each measured quantum coherent trajectory, we separately identify energy changes of the qubit as heat and work, and verify the first law of thermodynamics for an open quantum system. We further establish the consistency of these results by comparison with the master equation approach and the two-projective-measurement scheme, both for open and closed dynamics, with the help of a quantum feedback loop that compensates for the exchanged heat and effectively isolates the qubit.

P6290Enhanced IL-6/pSTAT3/fibroblast signaling pathway contributes to spontaneous postoperative atrial fibrillation in a novel simulated cardiac surgery mouse model

Background

Cumulative evidences have shown that IL-6 in atrium might play an important role in the pathogenesis of postoperative AF (POAF) via activation of atrial fibrosis in patients undergoing CABG. However, whether atria produces IL-6 after the stimulation of CABG and its causal relationship with spontaneous POAF (sPOAF) and its specific pathways is still unclear.

Purpose

To test the hypothesis that atrium will produce IL-6 after CABG and causes sustained sPOAF (ssPOAF) through activating pSTAT3-mediated fibroblast proliferation.

Methods

To determine the causal relationship between IL-6 and sPOAF, IL-6−/− and wild type (WT) mice were both divided into three groups (10 mice/group): CABG group (NAI, mimic CABG), anti-inflammatory group (AI, mimic CABG with pericardial administration of methylprednisolone for 3 days via chest tube), and control group (anesthesia only). Mice were monitored for ssPOAF for 7 days using implanted telemetry device. Another two sets of mice, using the same models mentioned above, were euthanatized at 48th hours postoperatively. The atria of one set animals were excised and separated into pericardium (PC), pulmonary vein (PV), left atrium (LA), and right atrium (RA) and cultured for 4 hours. IL-6 levels in the supernatant were measured at 10 min and 4 hours of culture using ELISA test. The region producing the largest amount of IL-6 in the other set of animals was harvested for analyzing expressions of IL-6, pSTAT3/STAT3, connexin 43 and 40, fibroblast deposition, and collagen I and III. Path analysis was performed to determine the causal relationship of CABG induced IL-6 release, pSTAT3/fibroblast signaling, and the onset of ssPOAF.

Results

40% NAI-WT mice developed ssPOAF (Figure 1A) which was completely protected in IL-6−/− and AI groups. IL-6 was produced by all 4 atrial regions at 4hrs after CABG stimulation with the LA producing the highest amount. Western blotting (Figure 1B), RT-CPR, Masson staining, and immunofluorescence all showed a significantly upregulation of IL-6, pSTAT3/STAT3, fibroblasts, collagen I and III, and downregulation of Cx40 an 43 in NAI-WT mice, but not in IL-6−/− and AI mice. IL-6 was colocalized with vimentin to a large extent in cytoplasm (Figure 1C). IL-6 had strong positive correlation with pSTAT3/STAT3, collagen I and III (all r>0.700, P<0.001), moderate and weak negative correlation with Cx40 and 43 (r=−0.505, P<0.001; r=−0.307, P=0.048, respectively). Path analysis (Figure 1D) revealed that every 1 unit increase in IL-6 upregulated a 0.589 unit increase in ssPOAF, which was mediated by pSTAT3/collagen indirectly and collagen I/ collagen III directly.

Conclusion

Our study, for the first time, to the best of our knowledge, established a novel pathophysiological role of IL-6/pSTAT3/fibroblast signaling in the pathogenesis of ssPOAF and demonstrated that inhibition of atrial IL-6 might be a potential novel sPOAF prevention strategy.

Acknowledgement/Funding

The National Natural Science Foundation (No.81170170)

Characterizing a Statistical Arrow of Time in Quantum Measurement Dynamics

In both thermodynamics and quantum mechanics, the arrow of time is characterized by the statistical likelihood of physical processes. We characterize this arrow of time for the continuous quantum measurement dynamics of a superconducting qubit. By experimentally tracking individual weak measurement trajectories, we compare the path probabilities of forward and backward-in-time evolution to develop an arrow of time statistic associated with measurement dynamics. We compare the statistics of individual trajectories to ensemble properties showing that the measurement dynamics obeys both detailed and integral fluctuation theorems, thus establishing the consistency between microscopic and macroscopic measurement dynamics.

Critical care usage after major gastrointestinal and liver surgery: a prospective, multicentre observational study

BACKGROUND

Patient selection for critical care admission must balance patient safety with optimal resource allocation. This study aimed to determine the relationship between critical care admission, and postoperative mortality after abdominal surgery.

METHODS

This prespecified secondary analysis of a multicentre, prospective, observational study included consecutive patients enrolled in the DISCOVER study from UK and Republic of Ireland undergoing major gastrointestinal and liver surgery between October and December 2014. The primary outcome was 30-day mortality. Multivariate logistic regression was used to explore associations between critical care admission (planned and unplanned) and mortality, and inter-centre variation in critical care admission after emergency laparotomy.

RESULTS

Of 4529 patients included, 37.8% (n=1713) underwent planned critical care admissions from theatre. Some 3.1% (n=86/2816) admitted to ward-level care subsequently underwent unplanned critical care admission. Overall 30-day mortality was 2.9% (n=133/4519), and the risk-adjusted association between 30-day mortality and critical care admission was higher in unplanned [odds ratio (OR): 8.65, 95% confidence interval (CI): 3.51-19.97) than planned admissions (OR: 2.32, 95% CI: 1.43-3.85). Some 26.7% of patients (n=1210/4529) underwent emergency laparotomies. After adjustment, 49.3% (95% CI: 46.8-51.9%, P<0.001) were predicted to have planned critical care admissions, with 7% (n=10/145) of centres outside the 95% CI.

CONCLUSIONS

After risk adjustment, no 30-day survival benefit was identified for either planned or unplanned postoperative admissions to critical care within this cohort. This likely represents appropriate admission of the highest-risk patients. Planned admissions in selected, intermediate-risk patients may present a strategy to mitigate the risk of unplanned admission. Substantial inter-centre variation exists in planned critical care admissions after emergency laparotomies.