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Abstract Preharvest sprouting (PHS) is an undesirable trait that decreases yield and quality in rice production. Understanding the genes and regulatory mechanisms underlying PHS is of great significance for breeding PHS-resistant rice. In this study, we identified a mutant, preharvest sprouting 39 (phs39), that exhibited an obvious PHS phenotype in the field. MutMap+ analysis and transgenic experiments demonstrated that OsAAH, which encodes allantoate amidohydrolase, is the causal gene of phs39 and is essential for PHS resistance. OsAAH was highly expressed in roots and leaves at the heading stage and gradually increased and then weakly declined in the seed developmental stage. OsAAH protein was localized to the endoplasmic reticulum, with a function of hydrolyzing allantoate in vitro. Disruption of OsAAH increased the levels of ureides (allantoate and allantoin) and activated the tricarboxylic acid (TCA) cycle, and thus increased energy levels in developing seeds. Additionally, the disruption of OsAAH significantly increased asparagine, arginine, and lysine levels, decreased tryptophan levels, and decreased levels of indole-3-acetic acid (IAA) and abscisic acid (ABA). Our findings revealed that the OsAAH of ureide catabolism is involved in the regulation of rice PHS via energy and hormone metabolisms, which will help to facilitate the breeding of rice PHS-resistant varieties.

Background & Aims: The vast majority of studies evaluating differences in on-treatment risks of hepatocellular carcinoma (HCC) in patients with chronic hepatitis B (CHB) have been conducted in Asia. Data on the course of CHB on antiviral therapy among predominantly non-Asian populations is less well described. We aimed to evaluate overall risks of cirrhosis and HCC and the influence of baseline factors on this risk among a predominantly non-Asian cohort of patients with CHB in the US. Methods: Using longitudinal data from the national Veterans Affairs database, we evaluated the incidence of cirrhosis or HCC among adults with non-cirrhotic CHB on continuous antiviral therapy. Cumulative incidence functions and adjusted Cox proportional hazards models employed competing risks methods and evaluated overall risk and predictors of developing cirrhosis or HCC while on treatment. Results: Among 2,496 patients with non-cirrhotic CHB (39.1% African American, 38.4% non-Hispanic White, 18.8% Asian, mean age 58.0 ± 13.4 years), the overall incidences of cirrhosis and HCC were 3.99 per 100 person-years (95% CI 3.66-4.35) and 0.43 per 100 person-years (95% CI 0.33-0.54), respectively. The highest incidences of cirrhosis and HCC were observed in non-Hispanic White patients (5.74 and 0.52 per 100 person-years, respectively), which were significantly higher than in Asian patients (1.93 and 0.17 per 100 person-years, respectively, p

Continual learning aims to avoid catastrophic forgetting and effectively leverage learned experiences to master new knowledge. Existing gradient projection approaches impose hard constraints on the optimization space for new tasks to minimize interference, which simultaneously hinders forward knowledge transfer. To address this issue, recent methods reuse frozen parameters with a growing network, resulting in high computational costs. Thus, it remains a challenge whether we can improve forward knowledge transfer for gradient projection approaches using a fixed network architecture. In this work, we propose the Restricted Orthogonal Gradient prOjection (ROGO) framework. The basic idea is to adopt a restricted orthogonal constraint allowing parameters optimized in the direction oblique to the whole frozen space to facilitate forward knowledge transfer while consolidating previous knowledge. Our framework requires neither data buffers nor extra parameters. Extensive experiments have demonstrated the superiority of our framework over several strong baselines. We also provide theoretical guarantees for our relaxing strategy.

Glioma is a primary high malignant intracranial tumor with poorly understood molecular mechanisms. Previous studies found that both DNA methylation modification and gene alternative splicing (AS) play a key role in tumorigenesis of glioma, and there is an obvious regulatory relationship between them. However, to date, no comprehensive study has been performed to analyze the influence of DNA methylation level on gene AS in glioma on a genome-wide scale. Here, we performed this study by integrating DNA methylation, gene expression, AS, disease risk methylation at position, and clinical data from 537 low-grade glioma (LGG) and glioblastoma (GBM) individuals. We first conducted a differential analysis of AS events and DNA methylation positions between LGG and GBM subjects, respectively. Then, we evaluated the influence of differential methylation positions on differential AS events. Further, Fisher’s exact test was used to verify our findings and identify potential key genes in glioma. Finally, we performed a series of analyses to investigate influence of these genes on the clinical prognosis of glioma. In total, we identified 130 glioma-related genes whose AS significantly affected by DNA methylation level. Eleven of them play an important role in glioma prognosis. In short, these results will help to better understand the pathogenesis of glioma.

Multiple sclerosis (MS) is an autoimmune disease characterized by inflammatory demyelinating lesions in the central nervous system. Recently, the dysregulation of alternative splicing (AS) in the brain has been found to significantly influence the progression of MS. Moreover, previous studies demonstrate that many MS-related variants in the genome act as the important regulation factors of AS events and contribute to the pathogenesis of MS. However, by far, no genome-wide research about the effect of genomic variants on AS events in MS has been reported. Here, we first implemented a strategy to obtain genomic variant genotype and AS isoform average percentage spliced-in values from RNA-seq data of 142 individuals (51 MS patients and 91 controls). Then, combing the two sets of data, we performed a cis-splicing quantitative trait loci (sQTLs) analysis to identify the cis-acting loci and the affected differential AS events in MS and further explored the characteristics of these cis-sQTLs. Finally, the weighted gene coexpression network and gene set enrichment analyses were used to investigate gene interaction pattern and functions of the affected AS events in MS. In total, we identified 5835 variants affecting 672 differential AS events. The cis-sQTLs tend to be distributed in proximity of the gene transcription initiation site, and the intronic variants of them are more capable of regulating AS events. The retained intron AS events are more susceptible to influence of genome variants, and their functions are involved in protein kinase and phosphorylation modification. In summary, these findings provide an insight into the mechanism of MS.

We propose and numerically analyze a broadband and high extinction ratio mode converter to achieve the mode conversion between the fundamental transverse electric mode (TE0) and the first-order transverse magnetic mode (TM1). The mode converter is achieved by using the tapered hybrid plasmonic waveguide which the metal is directly covered on the Si waveguide without a thin low-index layer. After optimizing the structure of the tapered hybrid plasmonic waveguide, a wide operation bandwidth of 100 nm is obtained with the extinction ratio of the TM1 mode and TE0 mode larger than 20 dB in the output Si waveguide for the forward propagation. And for the back propagation, the operation bandwidth over 65 nm is obtained with the extinction ratio larger than 20 dB in the output Si waveguide. The whole footprint of the mode converter is only 0.8 × 11 μm2. Fabrication tolerance analysis is also demonstrated.

Hand, foot, and mouth disease (HFMD) is well recognized as one of the major threats to children's health globally. The increasing complexity of the etiology of HFMD still challenges disease control in China. There is little surveillance of the molecular epidemiological characteristics of the enteroviruses (EVs) that cause HFMD in Neijiang city or the Sichuan Basin area in Southwest China. In this study, demographic and epidemiological information for 14,928 probable HFMD cases was extracted and analyzed to describe the epidemic features of HFMD in Neijiang city from Jan 2010 to Dec 2017. The swab samples of select probable HFMD cases from 2012 to 2017 were tested by reverse transcription (RT) real-time PCR to identify the serotype distribution of EVs, and 110 randomly selected RT-real-time PCR positive samples were then amplified and analyzed for the VP1 or VP4 regions of EVs to further analyze the phylogenetic characteristics of the circulating strains in this area. The eight-year average annual incidence was 49.82 per 100,000 in Neijiang. The incidence rates varied between 19.51 and 70.73 per 100,000, demonstrating peaks of incidence in even-number years (2012, 2014 and 2016). The median age of the probable cases was 27 months and the interquartile range (25th to 75th percentile) of ages for the probable HFMD cases was between 14 and 42 months. The male-to-female ratio of the probable HFMD cases was 1.47:1, and scattered children were the major population classification (81.7%). Two epidemic peaks were observed: one major peak between April and July and the other lesser peak between October and December. Of 6513 probable cases tested with RT-real-time PCR, 4015 (61.6%) were positive for enterovirus with the serotype distribution as follows: EV71+, 30.1% (n = 1210); CV-A16+, 28.7% (n = 1154) and a sole pan-enterovirus+, 41.1% (n = 1651). A total of 91 cases (82.7%, 91/110) were successfully amplified and underwent phylogenetic analysis: all EV71+ cases were C4a serotype (n = 23/30); all CV-A16+ cases were B2b serotype (n = 24/30); of 42 sole pan-enterovirus+ samples, 20 were CV-A6, 14 were CV-A10 and the rest within this group were CV-A4 (n = 4), CV-A8 (n = 2), CV-A9 (n = 1) and CV-B3 (n = 1). Our findings provide important evidence that aids the improvement of strategies for vaccination against HFMD and comprehensive disease control in China.

The thermal stress due to the thermal expansion mismatch could induce crystallographic defects such as buckling and cracking and degrade device performance. In this paper, the thermal stress distribution in a laser array structure selectively grown on V-groove-patterned Si substrates was investigated by two-dimension finite-element method. Surprisingly, unexpected results are observed that the top of the InGaAs active layer and the most region of the InP cap layer are in compression, which is far different from the thermal stress distribution in planar structures. Two mechanisms have been proposed and modeled to explain the difference—(i) the width of uncoalesced layers is smaller than that of the Si substrate, which causes thermal stress to change in epitaxial layers, and (ii) thermal stress in the InGaAs and InP layers is affected by the V-groove structure. The results show that whether or not the epitaxial layers are coalesced has significant effect on the thermal stress distribution. The effect of the height of the V-groove, the height and the width of the SiO2 mask on the thermal stress distribution was also studied. It is found that the height of V-groove and the height of SiO2 mask play a critical role in the stress distribution. These findings are useful for the optimal designs for the laser array and provide an important step towards the realization of photonic integration circuits on silicon.

INTRODUCTION: Hepatic steatosis is highly prevalent in people living with HIV. It remains unclear whether HIV in patients with metabolic dysfunction-associated steatotic liver disease (MASLD) is associated with greater risks of liver disease progression and cardiovascular disease (CVD). We aim to evaluate the impact of HIV infection on risks of liver and CVD outcomes among US Veterans with MASLD. METHODS: Using national Veterans Administration data from 2010 to 2022, we created a propensity score-matched cohort of MASLD patients with vs without HIV. Primary outcomes were incidence of cirrhosis and hepatocellular carcinoma (HCC) among patients with vs without HIV and patients with MASLD-HIV on antiretroviral therapy (ART) vs not on ART. Secondary outcomes included incidence of major adverse cardiovascular events and overall survival. RESULTS: The propensity-matched cohort included 920 MASLD patients with HIV and 920 MASLD patients without HIV and was similar in demographics and comorbidities. Compared with MASLD patients without HIV, incidences of cirrhosis and HCC were similar among MASLD with HIV. Compared with MASLD patients without HIV, incidence of major adverse cardiovascular event was higher among MASLD patients with HIV (5.18 vs 4.48 per 100 person-years, P = 0.03). Overall 5-year survival was significantly lower among MASLD patients with HIV and even lower among those not on ART. DISCUSSION: Among US Veterans with MASLD, concurrent HIV infection, and particularly not being on ART, is associated with greater risks of CVD and decreased overall survival. No differences in risks of cirrhosis or HCC were observed. [ABSTRACT FROM AUTHOR]

In this paper, l1/2-norm method is used to replace the traditional l1-norm to improve the compressed sensing technique. Numerical experiments and fan/compressor tests were performed to validate the applicability and robustness of the CS method based on l1/2-norm. Numerical experiments show that l1/2-norm method can effectually eliminate the spurious mode peaks generated by failed recovery of l1-norm method. Further study with random sensor failure shows the stronger robustness and applicability of l1/2-norm method. In the low-order acoustic mode detection experiment on cooling fan, 24 sensors were used to conduct mode decomposition at blade passing frequency (BPF). The recovered signal using l1/2-norm method was sparser than that using l1-norm method. In the case two sensors were randomly removed as failed sensors, the deviation between results of l1/2-norm method and original signal was also found smaller. In the condition that more sensors failed and l1-norm method did not work properly, l1/2-norm method could still detect the main mode. For further validation, the data from a high-order aerodynamic pressure mode detection experiment on axial compressor with two sensors damaged was processed through l1/2-norm method. The mode decomposition results at both BPF and the rotating instability frequency (RIF) agreed with the conclusion of the first experiment. Numerical experiments and fan/compressor tests show that using l1/2-norm can significantly improve the application and robustness of compressed sensing in mode detection. [ABSTRACT FROM AUTHOR]

The inaccuracy of anthropogenic emission inventory on a high-resolution scale due to insufficient basic data is one of the major reasons for the deviation between air quality model and observation results. A bottom-up approach, as a typical emission inventory estimation approach, requires a lot of human labor and material resources, and a top-down approach focuses on individual pollutants that can be measured directly and relies heavily on traditional numerical modelling. Lately, deep neural network has achieved rapid development due to its high efficiency and non-linear expression ability. In this study, we proposed a novel method to model the dual relationship between emission inventory and pollution concentration for emission inventory estimation. Specifically, we utilized a neural network based comprehensive chemical transport model (NN-CTM) to learn the complex correlation between emission and air pollution. We further updated the emission inventory based on backpropagating the gradient of the loss function measuring the deviation between NN-CTM and observations from surface monitors. We first mimicked the CTM model with neural networks (NN) and achieved a relatively good representation of CTM with similarity reaching 95%. To reduce the gap between CTM and observations, the NN model would suggest an updated emission of NOx, NH3, SO2, VOC and primary PM2.5 which changes by -1.34%, -2.65%, -11.66%, -19.19% and 3.51%, respectively, on average of China. Such ratios of NOx and PM2.5 are even higher (~10%) particularly in Northwest China where suffers from large uncertainties in original emissions. The updated emission inventory can improve model performance and make it closer to observations. The mean absolute error for NO2, SO2, O3 and PM2.5 concentrations are reduced significantly by about 10%~20%, indicating the high feasibility of NN-CTM in terms of significantly improving both the accuracy of emission inventory as well as the performance of air quality model. [ABSTRACT FROM AUTHOR]

Based on the field survey, this paper analyzes the relationship between groundwater and ecological environment in arid and semiarid areas in northwest China. Groundwater in the arid and semiarid areas is a natural resource with economic and ecological values. The concept of the ecological value of groundwater is firstly presented. This ecological value can be reflected in four aspects: (1) the maintenance of base flow in rivers and areas of lakes and wetland; (2) the supply of physiological water demanded by vegetations; (3) the regulation of soil moisture and salt content; and (4) the stability of the geological environment (such as land subsidence etc.). In addition, the threshold system between the ecological environment and multi-dimensional indices as variations in levels of the groundwater table, groundwater quality, water and salt content in the vadose zone as well as groundwater exploitation, are proposed in the arid and semiarid areas. It is expected that the system could provide a scientific basis and technological support for the regulation of the groundwater status and the maintenance of sustainable development of the ecological environment and utilization of water resources. [ABSTRACT FROM AUTHOR]