Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

BACKGROUND: Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress. RESULTS: To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS. CONCLUSIONS: Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-431) contains supplementary material, which is available to authorized users

Entropy-driven Sampling and Training Scheme for Conditional Diffusion Generation

Denoising Diffusion Probabilistic Model (DDPM) is able to make flexible conditional image generation from prior noise to real data, by introducing an independent noise-aware classifier to provide conditional gradient guidance at each time step of denoising process. However, due to the ability of classifier to easily discriminate an incompletely generated image only with high-level structure, the gradient, which is a kind of class information guidance, tends to vanish early, leading to the collapse from conditional generation process into the unconditional process. To address this problem, we propose two simple but effective approaches from two perspectives. For sampling procedure, we introduce the entropy of predicted distribution as the measure of guidance vanishing level and propose an entropy-aware scaling method to adaptively recover the conditional semantic guidance. For training stage, we propose the entropy-aware optimization objectives to alleviate the overconfident prediction for noisy data.On ImageNet1000 256x256, with our proposed sampling scheme and trained classifier, the pretrained conditional and unconditional DDPM model can achieve 10.89% (4.59 to 4.09) and 43.5% (12 to 6.78) FID improvement respectively. The code is available at https://github.com/ZGCTroy/ED-DPM.Comment: 24 pages, 8 figure

Mapping Regional Turbulent Heat Fluxes via Assimilation of MODIS Land Surface Temperature Data into an Ensemble Kalman Smoother Framework

Estimation of turbulent heat fluxes via variational data assimilation (VDA) approaches has been the subject of several studies. The VDA approaches need an adjoint model that is difficult to derive. In this study, remotely sensed land surface temperature (LST) data from the Moderate Resolution Imaging Spectroradiometer (MODIS) are assimilated into the heat diffusion equation within an ensemble Kalman smoother (EnKS) approach to estimate turbulent heat fluxes. The EnKS approach is tested in the Heihe River Basin (HRB) in northwest China. The results show that the EnKS approach can estimate turbulent heat fluxes by assimilating low temporal resolution LST data from MODIS. The findings indicate that the EnKS approach performs fairly well in various hydrological and vegetative conditions. The estimated sensible (H) and latent (LE) heat fluxes are compared with the corresponding observations from large aperture scintillometer systems at three sites (namely, Arou, Daman, and Sidaoqiao) in the HRB. The turbulent heat flux estimates from EnKS agree reasonably well with the observations, and are comparable to those of the VDA approach. The EnKS approach also provides statistical information on the H and LE estimates. It is found that the uncertainties of H and LE estimates are higher over wet and/or densely vegetated areas (grassland and forest) compared to the dry and/or slightly vegetated areas (cropland, shrubland, and barren land)

Neutron Spin Resonance in the Heavily Hole-doped KFe2_{2}As2_{2} Superconductor

We report high-resolution neutron scattering measurements of the low energy spin fluctuations of KFe$_{2}$As$_{2}$, the end member of the hole-doped Ba$_{1-x}$K$_x$Fe$_2$As$_2$ family with only hole pockets, above and below its superconducting transition temperature $T_c$ ($\sim$ 3.5 K). Our data reveals clear spin fluctuations at the incommensurate wave vector ($0.5\pm\delta$, 0, $L$), ($\delta$ = 0.2)(1-Fe unit cell), which exhibit $L$-modulation peaking at $L=0.5$. Upon cooling to the superconducting state, the incommensurate spin fluctuations gradually open a spin-gap and form a sharp spin resonance mode. The incommensurability ($2\delta$ = 0.4) of the resonance mode ($\sim1.2$ meV) is considerably larger than the previously reported value ($2\delta$ $\approx0.32$) at higher energies ($\ge\sim6$ meV). The determination of the momentum structure of spin fluctuation in the low energy limit allows a direct comparison with the realistic Fermi surface and superconducting gap structure. Our results point to an $s$-wave pairing with a reversed sign between the hole pockets near the zone center in KFe$_{2}$As$_{2}$.Comment: Accepted for publication in Physical Review Letter

Effects of Loading-Dose Statins Combined with PCSK9 Inhibitor Pre-Treatment before Primary Percutaneous Coronary Intervention on the Short-Term Prognosis in Patients with ST-Segment Elevation Myocardial Infarction

Objective: This study was aimed at investigating the effects of preoperative treatment with a loading dose of statins combined with a PCSK9 inhibitor on coronary blood perfusion and short-term cardiovascular adverse events in patients with ST-segment elevation myocardial infarction (STEMI). Method: Sixty-five patients with STEMI who had visited the Shanxi Cardiovascular Disease Hospital between May 2018 and May 2021 were enrolled in the study. The enrolled patients had no history of oral statins or antiplatelet therapy. The patients were divided into a combined treatment group (loading dose of statins combined with PCSK9 inhibitors, 35 patients) and a routine treatment group (loading dose of statins only, 30 patients). The primary endpoints were thrombolysis in myocardial infarction (TIMI) blood flow grading, corrected TIMI frame count (CTFC), and TIMI myocardial perfusion grading (TMPG), immediately after and 30 days after the operation. The secondary endpoint was a composite endpoint of cardiovascular death, nonfatal myocardial infarction, and target vessel revascularization 30 days after the operation. Results: The combined treatment group had significantly lower CTFC (14.09±8.42 vs 26±12.42, P=0.04) and better TMPG (2.74±0.61 vs 2.5±0.73, P=0.04) than the routine treatment group immediately after the operation. Similarly, the combined treatment group had a significantly lower CTFC (16.29±7.39 vs 26.23±11.53, P=0.04) and significantly better TMPG (2.94±0.24 vs 2.76±0.43, P=0.01) than the routine treatment group 1 month after the operation. Conclusion: Preoperative treatment with a loading dose of high-intensity statins combined with PCSK9 inhibitors increased coronary blood flow and myocardial perfusion after emergency thrombus aspiration in patients with STEMI. However, the treatment did not significantly decrease the incidence of cardiovascular death, nonfatal myocardial infarction, or target vessel revascularization