Accuracy of 3.0T magnetic resonance angiography for the detection of arteriovenous fistula dysfunction in hemodialysis patients requiring interventional therapy: a prospective study.

Background: Color Doppler ultrasonography (CDUS) is feasible to detect arteriovenous fistula (AVF) dysfunction in hemodialysis patients but is not sufficient to map the structure of fistula required for interventions. This study is designed to evaluate the diagnostic accuracy of three-dimensional time-of-flight magnetic resonance angiography (TOF-MRA) at 3.0T versus CDUS for AVF dysfunction, by using digital subtraction angiography (DSA) as reference. Methods: This prospective study enrolled 68 consecutive patients with dysfunctional AVF who underwent both CDUS and TOF-MRA at Shanghai Sixth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine. The analysis of the dysfunctional AVFs was divided into three regions: the feeding artery, fistula and draining veins. In the whole- and per-regional-based analyses, two observers who were blinded to the clinical and DSA results independently analyzed all CDUS and TOF-MRA datasets. The image quality and stenosis severity of the lesions on TOF-MRA were evaluated. A receiver operating characteristic curve was applied to analyze the detection of AVF dysfunction with TOF-MRA. Results: A total of 204 vessel regions were evaluated. The whole-region-based image quality of TOF-MRA was poorer in patients with a total occlusion (1.8±0.8) than in those with stenosis (2.7±0.6, P<0.001). In the whole-region analyses, TOF-MRA had higher sensitivity [99.1% (94.6-100.0%) vs. 82.9% (74.6-89.0%), P<0.001] and similar specificity [93.1% (85.0-97.1%) vs. 94.3% (86.5-97.9%), P=0.755] than CDUS. The per-region-based analyses showed that TOF-MRA yielded higher sensitivity [fistula region, 98.1% (88.4-99.9%) vs. 80.8% (67.0-89.9%); P=0.004; draining vein region, 100.0% (92.5-100.0%) vs. 85.0% (72.9-2.5%); P=0.003] and similar specificity [fistula region, 88.2% (62.3-97.8%) vs. 88.2% (62.3-97.9%); P>0.99; draining vein region, 100.0% (59.8-100.0%) vs. 87.5% (46.7-99.3%); P>0.99] than CDUS. Sensitivity and specificity of TOF-MRA were comparable to those of CDUS in feeding artery region. Conclusions: TOF-MRA is a feasible and accurate method to display AVF dysfunction in hemodialysis patients, and this method might fulfill the endovascular treatment planning requirements.

Tanshinone IIA Regulates Synaptic Plasticity in Mg2+-Free-Induced Epileptic Hippocampal Neurons via the PI3K/Akt Signaling Pathway.

BACKGROUND: Tanshinone IIA (TSIIA) is an element of the effective ingredients of Salvia miltiorrhiza Bunge (Labiatae), exhibits a significant therapeutic effect in brain neuroprotection. The focus of this study was the examination of synaptic plasticity of in Mg2+-free-induced epileptic hippocampus neurons and how TSIIA protects against it. METHODS: The purity of the primary hippocampal neurons extracted from Sprague Dawley rats was assessed within 24 hours by microtubule-associated protein (MAP2) immunofluorescence staining. A hippocampal neuron model for Mg2+-free-induced spontaneous recurrent epileptiform discharge was developed, five experimental groups were then randomized: blank (Blank), model (Model), TSIIA (TSIIA, 20 µM), LY294002 (LY294002, 25 µM), and TSIIA+LY294002 (TSIIA+LY294002, 20 µM+25 µM). FIJI software was used to examine variations of neurite complexity, total length of hippocampal neurons, number of primary dendrites and density of dendritic spines. Developmental regulation brain protein (Drebrin) and brain-derived neurotrophic factor (BDNF) expression was evaluated using immunofluorescence staining and the relative expression of phospho-protein kinase B (p-Akt)/Akt, BDNF, synaptophysin (SYN) and postsynaptic density 95 (PSD-95) determined by Western blot. RESULTS: In contrast to the model group, TSIIA drastically reduced damage to synaptic plasticity of hippocampal neurons caused by epilepsy (p < 0.05). The TSIIA group showed a significant increase in the relative expression of PSD-95, SYN, BDNF, and p-Akt/Akt (p < 0.01). CONCLUSIONS: TSIIA was effective in reducing harm to the synaptic plasticity of hippocampal neurons induced by persistent status epilepticus, with the possible mechanism being regulation of the phosphatidylinositol 3-kinase 56 (PI3K)/Akt signaling pathway.

Experimental Investigation of Current Intensity and Feed Speed in Electrically Assisted Necking and Thickening of 5A02 Aluminum Alloy Tubes.

In order to further explore the forming limits of thin-wall tube necking and thickening, and obtain sufficient thickness of the tube in the thickening area, local electric pulse-assisted forming experiments were carried out to study the effects of current intensity and feed speed on the necking and thickening forming of thin-wall tube. The experimental results show that with the increase in current intensity, the temperature in the forming area of the tube increases, and the forming load for necking and thickening decreases. However, with the increase in feed speed, the overall forming load for necking and thickening increases in general, and the smaller feed speed is more conducive to forming. Taking into account the forming efficiency and electrode loss, the corresponding forming process window is obtained for the manufacturing of good parts. That is, during the necking stage, the current intensity shall not be less than 300 A, and the feed speed shall not exceed 10 mm/min. During the thickening stage, the current intensity should not be less than 1400 A, and the feed speed should not exceed 1 mm/min. The target part is finally formed, with an average wall thickness of 5.984 mm in the thickening zone and a thickening rate of 303.2%.

Safety and efficacy of protective stent insertion to prevent carotid blowout syndrome at the distal internal carotid artery in nasopharyngeal carcinoma patients: a comparison with endovascular occlusion.

Background: Carotid blowout syndrome (CBS) frequently occurs at the distal internal carotid artery (distal-ICA) in patients with nasopharyngeal carcinoma (NPC), and remedial treatments run a high risk for neurologic complications. A case-control study was conducted to evaluate the safety and efficacy of protective stent insertion at the distal-ICA to prevent CBS in NPC patients, with a comparison to endovascular coil occlusion. Methods: A total of 28 consecutive NPC patients at high risk of CBS from June 2019 to December 2021 in Shanghai Sixth People's Hospital (a tertiary institution) were retrospectively included and divided into a stent protection group and occlusion group. Technique feasibility, treatment outcomes and neurological deficiency were compared between the two groups by two-sample test. Kaplan-Meier analysis compared patients' survival rates at mid-term follow-up. Results: Stent insertion was performed in 15 patients and ICA occlusion in 13 patients. The technical success rate was 100% in both groups. Procedure-related ischemic stroke was identified in 2 patients (15.4%) in the occlusion group, compared with none in the stent protection group. Bleeding was encountered in one patient in the stent protection group and one patient in the occlusion group, each. During a median follow-up of 10.5 (range, 2-31) months, 3 patients (20%) showed asymptomatic in-stent occlusion in the stent protection group. Notably, the median survival time was significantly longer in the stent protection group than in the occlusion group (23.3 vs. 15.8 months, P=0.04). Conclusions: Protective stenting the distal-ICA was similarly effective in preventing CBS in NPC patients but was safer than endovascular occlusion of ICA.

Transcriptome Analysis Reveals Drought-Responsive Pathways and Key Genes of Two Oat (Avena sativa) Varieties.

To cope with the yield loss caused by drought stress, new oat varieties with greater drought tolerance need to be selected. In this study, two oat varieties with different drought tolerances were selected for analysis of their phenotypes and physiological indices under moderate and severe soil drought stress. The results revealed significant differences in the degree of wilting, leaf relative water content (RWC), and SOD and CAT activity between the two oat genotypes under severe soil drought stress; moreover, the drought-tolerant variety exhibited a significant increase in the number of stomata and wax crystals on the surface of both the leaf and guard cells; additionally, the morphology of the guard cells was normal, and there was no significant disruption of the grana lamella membrane or the nuclear envelope. Furthermore, transcriptome analysis revealed that the expression of genes related to the biosynthesis of waxes and cell-wall components, as well as those of the WRKY family, significantly increased in the drought-tolerant variety. These findings suggest that several genes involved in the antioxidant pathway could improve drought tolerance in plants by regulating the increase/decrease in wax and cell-wall constituents and maintaining normal cellular water potential, as well as improving the ability of the antioxidant system to scavenge peroxides in oats.

Optimization of building integrated energy scheduling using an improved genetic whale algorithm.

Renewable energy generation has become the general trend with increasing environmental problems. However, the instability of renewable energy generation and the diversification of user demand are highlighted and the optimization of energy scheduling has become the key to solve the problem. This study introduces an energy scheduling optimization model tailored for building integrated energy systems, encompassing elements like gas turbines, wind and solar modules, ground source heat pumps, electric vehicles, central air-conditioning, and energy storage. The model prioritizes economic efficiency and minimal carbon emissions by first collecting and pre-processing the data for the regional building conformance, and then utilizing an enhanced multi-objective genetic whale algorithm. Evaluations on a regional complex building highlighted the algorithm's robust convergence and stability. The resulting optimized scheduling effectively balances economic and environmental concerns, reducing costs by about 92.896 yuan per day on average and reducing carbon emissions by about 0.091 tons, promoting efficient system operation, reducing costs and mitigating environmental impacts.

Impact of leukoaraiosis on the infarct growth rate and clinical outcome in acute large vessel occlusion stroke after endovascular thrombectomy.

INTRODUCTION: As a marker of chronic cerebral small vessel disease, leukoaraiosis (LA) was reported to impact the recruitment of collaterals in acute ischemic stroke (AIS). We intended to explore the impact of LA on the infarct growth rate (IGR) and clinical outcome by impaired collateral development in AIS patients with large vessel occlusion (LVO) who underwent endovascular thrombectomy (EVT). PATIENTS AND METHODS: Two hundred thirty-six AIS patients who underwent EVT were retrospectively reviewed. The severity of LA was graded using the Fazekas scale with non-contrast CT. IGR was calculated by the acute core volume on CT perfusion divided by the time from stroke onset to imaging. The collateral status after LVO was assessed using the ASITN/SIR collateral scale. The clinical outcomes after EVT were evaluated using a modified Rankin Scale (mRS). The Alberta stroke program early CT score (ASPECTS), the National Institutes of Health Stroke Scale (NIHSS) score at admission, and the modified treatment in cerebral infarction (mTICI) score after EVT were also included. Correlations between those factors were analyzed. RESULTS: Patients with severe LA had significantly larger core volume on CTP (p = 0.022) and lower collateral grade (p < 0.001). Faster IGR was significantly associated with higher LA severity (adjusted odds ratio [aOR]: 1.53; 95% CI: 1.02-2.33; p = 0.046), higher NIHSS (aOR: 1.04; 95% CI: 1.00-1.09; p = 0.032) and impaired collaterals (aOR: 2.26; 95% CI: 1.27-4.03; p = 0.005). In mediation analysis, collaterals explained 33% of the effect of LA on fast IGR. There was correlation between the severity of LA and mRS (p = 0.007). DISCUSSION AND CONCLUSION: The increasing severity of LA is associated with impaired collateral status and fast infarct growth. These findings suggest that LA may become a predictive imaging biomarker for the likelihood of progression of tissue injury and clinical outcome after EVT in acute large vessel occlusion stroke.

Elucidation of N-/O-glycosylation and site-specific mapping of sialic acid linkage isomers of SARS-CoV-2 human receptor angiotensin-converting enzyme 2.

Human angiotensin-converting enzyme 2 (hACE2) is the primary receptor for cellular entry of SARS-CoV-2 into human host cells. hACE2 is heavily glycosylated and glycans on the receptor may play a role in viral binding. Thus, comprehensive characterization of hACE2 glycosylation could aid our understanding of interactions between the receptor and SARS-CoV-2 spike (S) protein, as well as provide a basis for the development of therapeutic drugs targeting this crucial interaction. Herein, 138 N-glycan compositions were identified, most of which are complex-type N-glycans, from seven N-glycosites of hACE2. Among them, 67% contain at least one sialic acid residue. At the level of glycopeptides, the overall quantification of sialylated glycan isomers observed on the sites N322 and N546 have a higher degree of NeuAc (α2-3)Gal (over 80.3%) than that of other N-glycosites (35.6-71.0%). In terms of O-glycans, 69 glycan compositions from 12 O-glycosites were identified, and especially, the C-terminus of hACE2 is heavily O-glycosylated. The terminal sialic acid linkage type of H1N1S1 and H1N1S2 are covered highly with α2,3-sialic acid. These findings could aid the investigation of the interaction between SARS-CoV-2 and human host cells.

IgG glycomic profiling identifies potential biomarkers for diagnosis of echinococcosis.

Echinococcosis caused by larval stage of the genus Echinococcus, is a serious and potentially fatal parasitic zoonosis distributed globally. The two types of the disease in human are cystic echinococcosis (CE) and alveolar echinococcosis (AE). As the biological and encysting characteristics of the parasite, early diagnosis remains to address. In the present study, we demonstrate the value of Immunoglobulin G (IgG) glycome as a potential diagnostic biomarker for echinococcosis. Serum IgG glycome profiles were analyzed by ultra-performance liquid chromatography in a cohort comprised of 127 echinococcosis patients, of them 98 were diagnosed as CE and 29 as AE. IgG N-glycome analysis in pretreatment serum of echinococcosis patients presents 25 glycans and 64 derived traits. Compared with IgG glycans of healthy control group, neutral glycans, fucosylation and agalactosylated N-glycans increased while sialylation and galactosylation decreased in echinococcosis patients. Combined with a machine-learning-based approach, we built three biomarker combinations to distinguish CE, AE and healthy controls. Meanwhile, galactosylation, sialylation and A2BG2S1 in IgG glycan profiles were evidently associated with different types of CE (from CE1 to CE5). Our findings suggest that the alterations in IgG N-glycome may be of value in CE and AE diagnosis and follow-up CE disease progress. The role of IgG N-glycans as diagnostic biomarker remains to be verified in future study.

Iron homeostasis imbalance and ferroptosis in brain diseases.

Brain iron homeostasis is maintained through the normal function of blood-brain barrier and iron regulation at the systemic and cellular levels, which is fundamental to normal brain function. Excess iron can catalyze the generation of free radicals through Fenton reactions due to its dual redox state, thus causing oxidative stress. Numerous evidence has indicated brain diseases, especially stroke and neurodegenerative diseases, are closely related to the mechanism of iron homeostasis imbalance in the brain. For one thing, brain diseases promote brain iron accumulation. For another, iron accumulation amplifies damage to the nervous system and exacerbates patients' outcomes. In addition, iron accumulation triggers ferroptosis, a newly discovered iron-dependent type of programmed cell death, which is closely related to neurodegeneration and has received wide attention in recent years. In this context, we outline the mechanism of a normal brain iron metabolism and focus on the current mechanism of the iron homeostasis imbalance in stroke, Alzheimer's disease, and Parkinson's disease. Meanwhile, we also discuss the mechanism of ferroptosis and simultaneously enumerate the newly discovered drugs for iron chelators and ferroptosis inhibitors.

Thrombus Enhancement Sign May Differentiate Embolism From Arteriosclerosis-Related Large Vessel Occlusion.

BACKGROUND AND PURPOSE: To evaluate whether the thrombus enhancement sign (TES) can be used to differentiate embolic large vessel occlusion (LVO) from in situ intracranial atherosclerotic stenosis (ICAS)-related LVO in the anterior circulation of patients with acute ischemic stroke (AIS). METHODS: Patients with LVO in the anterior circulation who underwent both non-contrast computed tomography (CT) and CT angiography and mechanical thrombectomy were retrospectively enrolled. Both embolic LVO (embo-LVO) and in situ ICAS-related LVO (ICAS-LVO) were confirmed by two neurointerventional radiologists after reviewing the medical and imaging data. TES was assessed to predict embo-LVO or ICAS-LVO. The associations between occlusion type and TES, along with clinical and interventional parameters, were investigated using logistic regression analysis and a receiver operating characteristic curve. RESULTS: A total of 288 patients with AIS were included and divided into an embo-LVO group (n=235) and an ICAS-LVO group (n=53). TES was identified in 205 (71.2%) patients and was more frequently observed in those with embo-LVO, with a sensitivity of 83.8%, specificity of 84.9%, and area under the curve (AUC) of 0.844. Multivariate analysis showed that TES (odds ratio [OR], 22.2; 95% confidence interval [CI], 9.4-53.8; P<0.001) and atrial fibrillation (OR, 6.6; 95% CI, 2.8-15.8; P<0.001) were independent predictors of embolic occlusion. A predictive model that included both TES and atrial fibrillation yielded a higher diagnostic ability for embo-LVO, with an AUC of 0.899. CONCLUSION: TES is an imaging marker with high predictive value for identifying embo- and ICAS-LVO in AIS and provides guidance for endovascular reperfusion therapy.

Core overestimation of CT perfusion in patients with cardiac insufficiency who had a stroke is mediated by impaired collaterals.

BACKGROUND: We hypothesized that left ventricular systolic dysfunction (LVSD) would lead to an ischemic core overestimation in patients with acute ischemic stroke (AIS), and impaired collateral status might partly mediate this effect. OBJECTIVE: A pixel-based analysis of CT perfusion (CTP) and follow-up CT was undertaken to investigate the optimum CTP thresholds for the ischemic core if overestimation was found. METHODS: A total of 208 consecutive patients with AIS with large vessel occlusion in the anterior circulation, who received initial CTP evaluation and successful reperfusion, were retrospectively analyzed and divided into an LVSD (left ventricular ejection fraction (LVEF) ratio <50%; n=40) and a normal cardiac function (LVEF≥50%; n=168) group. Ischemic core overestimation was considered when the CTP-derived core was larger than the final infarct volume. We investigated the relationship between cardiac function, probability for core overestimation, and collateral scores using mediation analysis. A pixel-based analysis was undertaken to define the optimum CTP thresholds for ischemic core. RESULTS: LVSD was independently associated with impaired collaterals (aOR=4.28, 95% CI 2.01 to 9.80, P<0.001) and core overestimation (aOR=2.52, 95% CI 1.07 to 5.72, P=0.030). In mediation analysis, the total effect on core overestimation is composed of the direct effect of LVSD (+17%, P=0.034) and the mediated indirect effect of collateral status (+6%, P=0.020). Collaterals explained 26% of the effect of LVSD on core overestimation. Compared with relative cerebral blood flow (rCBF) thresholds of <35%, <30%, and <20%, a rCBF <25% cut-off point had the highest correlation (r=0.91) and best agreement (mean difference 3.2±7.3 mL) with the final infarct volume to determine the CTP-derived ischemic core in patients with LVSD. CONCLUSIONS: LVSD increased the possibility of ischemic core overestimation on baseline CTP, partly due to impaired collateral status, and a stricter rCBF threshold should be considered.

Thrombus enhancement sign on CT angiography is associated with the first pass effect of stent retrievers.

BACKGROUND: The thrombus enhancement sign (TES) is thought to be associated with the source of the stroke and thrombus composition. We investigated whether this imaging sign along with other thrombus characteristics could be used to predict the successful first pass effect (FPE) of mechanical thrombectomy. METHODS: 246 consecutive patients with acute ischemic stroke in the anterior circulation with large vessel occlusion who underwent thrombectomy with a stent retriever and clot collection were included. Patients were divided into FPE (modified Thrombolysis in Cerebral Infarction (mTICI) grade 2c or 3)/non-FPE (mTICI 0-2b) and modified FPE (mFPE) (mTICI 2b-3)/non-mFPE (mTICI 0-2a) groups based on flow restoration after the first pass. TES presence, thrombus density, thrombus length, clot burden score, and thrombus composition were compared. The association between FPE and imaging biomarkers, along with clinical and interventional parameters, was investigated by univariate and multivariate analysis. RESULTS: FPE was achieved in 85 (34.6%) patients. TES presence was significantly lower in the FPE group (64.7% vs 80.7% in the non-FPE group, p=0.008) and mFPE group (69.1% vs 81.0% in the non-mFPE group, p=0.039). Histopathological examination revealed that TES (+) thrombi contained a higher fibrin/platelet proportion (50.9% vs 46.9% in TES (-) thrombi, p=0.029) and fewer erythrocytes (43.3% vs 47.3% in TES (-) thrombi, p=0.030). Thrombus characteristics, namely shorter thrombus length (p=0.032), higher erythrocyte proportions (p=0.026), and less fibrin/platelets (p=0.014), were confirmed in patients with FPE. In multivariable analysis, TES was the only independent predictor of FPE failure (OR 0.51, 95% CI 0.28 to 0.94; p=0.031). CONCLUSIONS: TES was independently associated with first pass angiographic failure in patients treated with a stent retriever.

Investigation of the mechanism of tanshinone IIA to improve cognitive function via synaptic plasticity in epileptic rats.

CONTEXT: Tanshinone IIA is an extract of Salvia miltiorrhiza Bunge (Labiatae) used to treat cardiovascular disorders. It shows potential anticonvulsant and cognition-protective properties. OBJECTIVE: We investigated the mechanism of tanshinone IIA on antiepileptic and cognition-protective effects in the model of epileptic rats. MATERIALS AND METHODS: Lithium chloride (LiCl)-pilocarpine-induced epileptic Wistar rats were randomly assigned to the following groups (n = 12): control (blank), model, sodium valproate (VPA, 189 mg/kg/d, positive control), tanshinone IIA low dose (TS IIA-L, 10 mg/kg/d), medium dose (TS IIA-M, 20 mg/kg/d) and high dose (TS IIA-H, 30 mg/kg/d). Then, epileptic behavioural observations, Morris water maze test, Timm staining, transmission electron microscopy, immunofluorescence staining, western blotting and RT-qPCR were measured. RESULTS: Compared with the model group, tanshinone IIA reduced the frequency and severity of seizures, improved cognitive impairment, and inhibited hippocampal mossy fibre sprouting score (TS IIA-M 1.50 ± 0.22, TS IIA-H 1.17 ± 0.31 vs. model 2.83 ± 0.31), as well as improved the ultrastructural disorder. Tanshinone IIA increased levels of synapse-associated proteins synaptophysin (SYN) and postsynaptic dense substance 95 (PSD-95) (SYN: TS IIA 28.82 ± 2.51, 33.18 ± 2.89, 37.29 ± 1.69 vs. model 20.23 ± 3.96; PSD-95: TS IIA 23.10 ± 0.91, 26.82 ± 1.41, 27.00 ± 0.80 vs. model 18.28 ± 1.01). DISCUSSION AND CONCLUSIONS: Tanshinone IIA shows antiepileptic and cognitive function-improving effects, primarily via regulating synaptic plasticity. This research generates a theoretical foundation for future research on potential clinical applications for tanshinone IIA.

Clot-based radiomics model for cardioembolic stroke prediction with CT imaging before recanalization: a multicenter study.

OBJECTIVES: To develop a clot-based radiomics model using CT imaging radiomic features and machine learning to identify cardioembolic (CE) stroke before mechanical thrombectomy (MTB) in patients with acute ischemic stroke (AIS). MATERIALS AND METHODS: This retrospective four-center study consecutively included 403 patients with AIS who sequentially underwent CT and MTB between April 2016 and July 2021. These were grouped into training, testing, and external validation cohorts. Thrombus-extracted radiomic features and basic information were gathered to construct a machine learning model to predict CE stroke. The radiological characteristics and basic information were used to build a routine radiological model. A combined radiomics and radiological features model was also developed. The performances of all models were evaluated and compared in the validation cohort. A histological analysis helped further assess the proposed model in all patients. RESULTS: The radiomics model yielded an area under the curve (AUC) of 0.838 (95% confidence interval [CI], 0.771-0.891) for predicting CE stroke in the validation cohort, significantly higher than the radiological model (AUC, 0.713; 95% CI, 0.636-0.781; p = 0.007) but similar to the combined model (AUC, 0.855; 95% CI, 0.791-0.906; p = 0.14). The thrombus radiomic features achieved stronger correlations with red blood cells (|rmax|, 0.74 vs. 0.32) and fibrin and platelet (|rmax|, 0.68 vs. 0.18) than radiological characteristics. CONCLUSION: The proposed CT-based radiomics model could reliably predict CE stroke in AIS, performing better than the routine radiological method. KEY POINTS: • Admission CT imaging could offer valuable information to identify the acute ischemic stroke source by radiomics analysis. • The proposed CT imaging-based radiomics model yielded a higher area under the curve (0.838) than the routine radiological method (0.713; p = 0.007). • Several radiomic features showed significantly stronger correlations with two main thrombus constituents (red blood cells, |rmax|, 0.74; fibrin and platelet, |rmax|, 0.68) than routine radiological characteristics.

Reference genome assemblies reveal the origin and evolution of allohexaploid oat.

Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.

Adversarial training for prostate cancer classification using magnetic resonance imaging.

Background: To use adversarial training to increase the generalizability and diagnostic accuracy of deep learning models for prostate cancer diagnosis. Methods: This multicenter study retrospectively included 396 prostate cancer patients who underwent magnetic resonance imaging (development set, 297 patients from Shanghai Jiao Tong University Affiliated Sixth People's Hospital and Eighth People's Hospital; test set, 99 patients from Renmin Hospital of Wuhan University). Two binary classification deep learning models for clinically significant prostate cancer classification [PM1, pretraining Visual Geometry Group network (VGGNet)-16-based model 1; PM2, pretraining residual network (ResNet)-50-based model 2] and two multiclass classification deep learning models for prostate cancer grading (PM3, pretraining VGGNet-16-based model 3; PM4: pretraining ResNet-50-based model 4) were built using apparent diffusion coefficient and T2-weighted images. These models were then retrained with adversarial examples starting from the initial random model parameters (AM1, adversarial training VGGNet-16 model 1; AM2, adversarial training ResNet-50 model 2; AM3, adversarial training VGGNet-16 model 3; AM4, adversarial training ResNet-50 model 4, respectively). To verify whether adversarial training can improve the diagnostic model's effectiveness, we compared the diagnostic performance of the deep learning methods before and after adversarial training. Receiver operating characteristic curve analysis was performed to evaluate significant prostate cancer classification models. Differences in areas under the curve (AUCs) were compared using Delong's tests. The quadratic weighted kappa score was used to verify the PCa grading models. Results: AM1 and AM2 had significantly higher AUCs than PM1 and PM2 in the internal validation dataset (0.84 vs. 0.89 and 0.83 vs. 0.87) and test dataset (0.73 vs. 0.86 and 0.72 vs. 0.82). AM3 and AM4 showed higher κ values than PM3 and PM4 in the internal validation dataset {0.266 [95% confidence interval (CI): 0.152-0.379] vs. 0.292 (95% CI: 0.178-0.405) and 0.254 (95% CI: 0.159-0.390) vs. 0.279 (95% CI: 0.163-0.396)} and test set [0.196 (95% CI: 0.029-0.362) vs. 0.268 (95% CI: 0.109-0.427) and 0.183 (95% CI: 0.015-0.351) vs. 0.228 (95% CI: 0.068-0.389)]. Conclusions: Using adversarial examples to train prostate cancer classification deep learning models can improve their generalizability and classification abilities.

Overexpression of GhABF3 increases cotton(Gossypium hirsutum L.) tolerance to salt and drought.

BACKGROUND: Plants suffer from various abiotic stresses during their lifetime, of which drought and salt stresses are two main factors limiting crop yield and quality. Previous studies have shown that abscisic acid (ABA) responsive element binding protein (AREB)/ ABRE binding factors (ABFs) in bZIP transcription factors are involved in plant stress response in an ABA-dependent manner. However, little is known about the properties and functions of AREB/ABFs, especially ABF3, in cotton. RESULTS: Here, we reported the cloning and characterization of GhABF3. Expression of GhABF3 was induced by drought,salt and ABA treatments. Silencing of GhABF3 sensitized cotton to drought and salt stress, which was manifested in decreased cellular antioxidant capacity and chlorophyll content. Overexpression of GhABF3 significantly improved the drought and salinity tolerance of Arabidopsis and cotton. Exogenous expression of GhABF3 resulted in longer root length and less leaf wilting under stress conditions in Arabidopsis thaliana. Overexpressing GhABF3 significantly improved salt tolerance of upland cotton by reducing the degree of cellular oxidation, and enhanced drought tolerance by decreasing leaf water loss rate. The increased expression of GhABF3 up-regulated the transcriptional abundance of downstream ABA-inducible genes under salt stress in Arabidopsis. CONCLUSION: In conclusion, our results demonstrated that GhABF3 plays an important role in plant drought and salt tolerance. Manipulation of GhABF3 by biotechnology might be an important strategy to alter the stress resistance of cotton.

Dynamic Quantitative Trait Loci Mapping for Plant Height in Recombinant Inbred Line Population of Upland Cotton.

Plant height (PH) is a key plant architecture trait for improving the biological productivity of cotton. Ideal PH of cotton is conducive to lodging resistance and mechanized harvesting. To detect quantitative trait loci (QTL) and candidate genes of PH in cotton, a genetic map was constructed with a recombinant inbred line (RIL) population of upland cotton. PH phenotype data under nine environments and three best linear unbiased predictions (BLUPs) were used for QTL analyses. Based on restriction-site-associated DNA sequence (RAD-seq), the genetic map contained 5,850 single-nucleotide polymorphism (SNP) markers, covering 2,747.12 cM with an average genetic distance of 0.47 cM. Thirty-seven unconditional QTL explaining 1.03-12.50% of phenotypic variance, including four major QTL and seven stable QTL, were identified. Twenty-eight conditional QTL explaining 3.27-28.87% of phenotypic variance, including 1 major QTL, were identified. Importantly, five QTL, including 4 stable QTL, were both unconditional and conditional QTL. Among the 60 PH QTL (including 39 newly identified), none of them were involved in the whole period of PH growth, indicating that QTL related to cotton PH development have dynamic expression characteristics. Based on the functional annotation of Arabidopsis homologous genes and transcriptome data of upland cotton TM-1, 14 candidate genes were predicted within 10 QTL. Our research provides valuable information for understanding the genetic mechanism of PH development, which also increases the economic production of cotton.