NMR Spectra Denoising with Vandermonde Constraints

Nuclear magnetic resonance (NMR) spectroscopy serves as an important tool to analyze chemicals and proteins in bioengineering. However, NMR signals are easily contaminated by noise during the data acquisition, which can affect subsequent quantitative analysis. Therefore, denoising NMR signals has been a long-time concern. In this work, we propose an optimization model-based iterative denoising method, CHORD-V, by treating the time-domain NMR signal as damped exponentials and maintaining the exponential signal form with a Vandermonde factorization. Results on both synthetic and realistic NMR data show that CHORD-V has a superior denoising performance over typical Cadzow and rQRd methods, and the state-of-the-art CHORD method. CHORD-V restores low-intensity spectral peaks more accurately, especially when the noise is relatively high.Comment: 10 pages, 9 figure

The Existence of Spanning Ended System on Claw-Free Graphs

We prove that every connected claw-free graph G contains a spanning k-ended system if and only if cl(G) contains a spanning k-ended system, where cl(G) denotes Ryjáček closure of G

CloudBrain-NMR: An Intelligent Cloud Computing Platform for NMR Spectroscopy Processing, Reconstruction and Analysis

Nuclear Magnetic Resonance (NMR) spectroscopy has served as a powerful analytical tool for studying molecular structure and dynamics in chemistry and biology. However, the processing of raw data acquired from NMR spectrometers and subsequent quantitative analysis involves various specialized tools, which necessitates comprehensive knowledge in programming and NMR. Particularly, the emerging deep learning tools is hard to be widely used in NMR due to the sophisticated setup of computation. Thus, NMR processing is not an easy task for chemist and biologists. In this work, we present CloudBrain-NMR, an intelligent online cloud computing platform designed for NMR data reading, processing, reconstruction, and quantitative analysis. The platform is conveniently accessed through a web browser, eliminating the need for any program installation on the user side. CloudBrain-NMR uses parallel computing with graphics processing units and central processing units, resulting in significantly shortened computation time. Furthermore, it incorporates state-of-the-art deep learning-based algorithms offering comprehensive functionalities that allow users to complete the entire processing procedure without relying on additional software. This platform has empowered NMR applications with advanced artificial intelligence processing. CloudBrain-NMR is openly accessible for free usage at https://csrc.xmu.edu.cn/CloudBrain.htmlComment: 11 pages, 13 figure

Effects of different fertilization conditions and different geographical locations on the diversity and composition of the rhizosphere microbiota of Qingke (Hordeum vulgare L.) plants in different growth stages

IntroductionThe excessive use of chemical fertilizer causes increasing environmental and food security crisis. Organic fertilizer improves physical and biological activities of soil. Rhizosphere microbiota, which consist of highly diverse microorganisms, play an important role in soil quality. However, there is limited information about the effects of different fertilization conditions on the growth of Qingke plants and composition of the rhizosphere microbiota of the plants.MethodsIn this study, we characterized the rhizosphere microbiota of Qingke plants grown in three main Qingke-producing areas (Tibet, Qinghai, and Gansu). In each of the three areas, seven different fertilization conditions (m1–m7, m1: Unfertilized; m2: Farmer Practice; m3: 75% Farmer Practice; m4: 75% Farmer Practice +25% Organic manure; m5: 50% Farmer Practice; m6: 50% Farmer Practice +50% Organic manure; m7: 100% Organic manure) were applied. The growth and yields of the Qingke plants were also compared under the seven fertilization conditions.ResultsThere were significant differences in alpha diversity indices among the three areas. In each area, differences in fertilization conditions and differences in the growth stages of Qingke plants resulted in differences in the beta diversity of the rhizosphere microbiota. Meanwhile, in each area, fertilization conditions, soil depths, and the growth stages of Qingke plants significantly affected the relative abundance of the top 10 phyla and the top 20 bacterial genera. For most of microbial pairs established through network analysis, the significance of their correlations in each of the microbial co-occurrence networks of the three experimental sites was different. Moreover, in each of the three networks, there were significant differences in relative abundance and genera among most nodes (i.e., the genera Pseudonocardia, Skermanella, Pseudonocardia, Skermanella, Aridibacter, and Illumatobacter). The soil chemical properties (i.e., TN, TP, SOM, AN, AK, CEC, Ca, and K) were positively or negatively correlated with the relative abundance of the top 30 genera derived from the three main Qingke-producing areas (p < 0.05). Fertilization conditions markedly influenced the height of a Qingke plant, the number of spikes in a Qingke plant, the number of kernels in a spike, and the fresh weight of a Qingke plant. Considering the yield, the most effective fertilization conditions for Qingke is combining application 50% chemical fertilizer and 50% organic manure.ConclusionThe results of the present study can provide theoretical basis for practice of reducing the use of chemical fertilizer in agriculture

The Spectral Radius for a Class of Double-Star-Like Tree Systems with Maximal Degree 4

We mainly study the properties of the 4-double-star-like tree, which is the generalization of star-like trees. Firstly we use graft transformation method to obtain the maximal and minimum extremal graphs of 4-double-star-like trees. Secondly, by the relations between the degree and second degree of vertices in maximal extremal graphs of 4-double-star-like trees we get the upper bounds of spectral radius of 4-double-star-like trees

VDR Agonist Prevents Diabetic Endothelial Dysfunction through Inhibition of Prolyl Isomerase-1-Mediated Mitochondrial Oxidative Stress and Inflammation

Background and aim. Upregulation of prolyl isomerase-1 (Pin1) protein expression and activity was associated with the pathogenesis of diabetic vasculopathy through induction of endothelial oxidative stress and inflammation. Moreover, VDR agonist protects against high glucose-induced endothelial apoptosis through the inhibition of oxidative stress. We aimed to explore the effects of the VDR agonist on diabetes-associated endothelial dysfunction and the role of Pin1 in this process. Methods. Streptozocin-induced diabetic mice were randomly treated with vehicle, VDR agonist (10 μg/kg/d, i.g., twice a week), or Pin1 inhibitor, Juglone (1 mg/kg/d, i.p., every other day), for eight weeks. In parallel, human umbilical vein endothelial cells (HUVECs) exposed to high-glucose condition were treated with 1,25-dihydroxyvitamin D3 and Juglone or vehicle for 72 hours. Organ chamber experiments were performed to assess endothelium-dependent relaxation to acetylcholine. Circulatory levels of Pin1, SOD, MDA, IL-1β, IL-6, and NO in diabetic mice, Pin1 protein expression and activity, subcellular distribution of p66Shc, and NF-κB p65 in high glucose-cultured HUVECs were determined. Results. Both VDR agonist and Juglone significantly improved diabetes-associated endothelial dysfunction and reduced high glucose-induced endothelial apoptosis. Mechanistically, the circulatory levels of SOD and NO were increased compared with those of vehicle-treated diabetic mice. Additionally, Pin1 protein expression and activity, p66Shc mitochondrial translocation, and NF-κB p65 in high glucose-cultured HUVECs were also inhibited by VDR agonist and Juglone. Knockdown of VDR abolished the inhibitory effects of VDR agonist on high glucose-induced upregulation of Pin1 protein expression and activity. Conclusions. VDR agonist prevents diabetic endothelial dysfunction through inhibition of Pin1-mediated mitochondrial oxidative stress and inflammation

Anti-Diabetic Atherosclerosis by Inhibiting High Glucose-Induced Vascular Smooth Muscle Cell Proliferation via Pin1/BRD4 Pathway

Background and purpose. Vascular smooth muscle cells (VSMC) proliferation and migration is the important pathological process of diabetic atherosclerosis. Bromine domain protein 4 (BRD4) is involved in cell proliferation and inflammatory disease. Pin1 enhances BRD4 stability and its transcriptional activity. This study aimed to explore the possible mechanism of Pin1/BRD4 in diabetic atherosclerosis. Methods. Diabetic Apoe-/- mice induced by streptozotocin were treated with vehicle, the Pin1 inhibitor juglone, or the BRD4 inhibitor JQ1 for 3 weeks. VSMCs were pretreated with juglone, JQ1, or vehicle for 45 min, and then exposed to high glucose for 48 h. Hematoxylin–eosin staining was performed to assess atherosclerotic plaques of the thoracic aorta. Western blotting was used to detect expression levels of Pin1, BRD4, cyclin D1, and matrix metalloproteinase-9 (MMP-9) in the thoracic aorta and VSMCs. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and transwell assay were used to measure proliferation and migration of VSMCs. Results. Juglone and JQ1 significantly improved atherosclerosis of diabetic Apoe-/- mice and reduced high glucose-induced VSMC proliferation and migration. Cyclin D1 and MMP-9 levels in the thoracic aorta were lower in diabetic Apoe-/- mice treated with juglone and JQ1 compared with vehicle-treated diabetic Apoe-/- mice. Additionally, BRD4 protein expression in high glucose-induced VSMCs was inhibited by juglone and JQ1. Upregulation of Pin1 expression by transduction of the Pin1 plasmid vector promoted BRD4 expression induced by high glucose, and stimulated proliferation and migration of VSMCs. Conclusions. Inhibition of Pin1/BRD4 pathway may improve diabetic atherosclerosis by inhibiting proliferation and migration of VSMCs

Parent-Adolescent Conflict, Depressive Symptoms, and Non-Suicidal Self-Injury among Chinese Adolescents: The Moderating Effect of the COMT Gene rs4680 Polymorphism

Existing research suggests that parent-adolescent conflict is associated with increased risk for adolescent non-suicidal self-injury (NSSI). However, adolescent NSSI reactions to parent-adolescent conflicts exhibit large individual differences. This study sought to explore whether depressive symptoms mediates the relationship between parent-adolescent conflict and adolescent NSSI, and whether this mediating process is moderated by the COMT gene rs4680 polymorphism. A total of 673 adolescents (364 males, 309 females) in the age range of 12 to 15 years (Meanage = 12.81 years, SD = 0.48) completed questionnaires regarding parent-adolescent conflict, depressive symptoms, and NSSI. Genomic DNA was extracted from saliva and buccal cells from each participant. Bootstrapping techniques displayed statistically significant moderated mediation. The results showed that the positive association between parent-adolescent conflict and adolescent NSSI was in fact mediated by depressive symptoms. Moreover, this indirect link was moderated by the COMT gene rs4680 polymorphism. Specifically, the risk effect of parent-adolescent conflict on adolescent NSSI via depressive symptoms was stronger for adolescents with Val/Val genotype than for those with Met/Met or Val/Met genotype. These findings underscore the importance of examining the interaction between genes and the environment to understand how and when parent-adolescent conflict impacts adolescent NSSI

Efficient generation of male germ-like cells derived during co-culturing of adipose-derived mesenchymal stem cells with Sertoli cells under retinoic acid and testosterone induction

Abstract Background Adipose-derived mesenchymal stem cells (ADMSCs) are considered an efficient and important candidate for male infertility treatment because they contain pluripotent stem cells, which can differentiate into all cells from three germ layers. However, the efficient generation of male germ-like cell (MGLCs) is one of the key issues, and little is known about the mechanisms underlying generation of MGLCs. Herein, we attempt to improve the efficient generation of MGLCs derived during co-culturing of rat ADMSCs with SCs under retinoic acid (RA) and testosterone (T) treatment. Methods ADMSCs isolated from male SD rat were induced into generation of MGLCs by using respective methods in vitro. Transwell insert system was used for co-culturing. Busulfan-induced non-obstructive azoospermia rat mode was used to evaluate spermatogenic recovery ability of treated ADMSCs. Besides, the relative gene expression level was detected by reverse transcription PCR, quantitative RT-PCR. The relative protein expression level was detected by western blot (WB) and immunostaining analysis. Results The results showed that ADMSCs co-cultured with TM4 cells under RA and T induction enhanced the formation of bigger and tightly packed MGLCs feature colonies in vitro. Moreover, the expression of male germ cell-related markers (Oct4, Stella, Ddx4, Dazl, PGP9.5, Stra8, and ITGα6) is significantly upregulated in TM4 cell-co-cultured ADMSCs in vitro and in busulfan-treated rat testis after injecting TM4 cell-treated ADMSCs for 2 months. Comparatively, the ADMSCs treated by TM4 cell with RA and T exhibited the highest expression of male germ cell-related markers. RA- and T-treated TM4 cell showed fewer dead cells and higher cytokine secretion than untreated groups. The protein expression level of TGFβ-SMAD2/3, JAK2-STAT3, and AKT pathways in ADMSCs co-cultured with TM4 cells under RA and T was higher than others. Whereas, downregulation of male germ cell-related marker expression subsequently inhibited the phosphorylation of SMAD2/3, JAK2, STAT3, and AKT. Conclusion These results suggested that TM4 cells could efficiently stimulate in vitro generation of MGLCs during co-culturing of ADMSCs under RA and T treatment. Conclusively, the ADMSCs co-cultured with TM4 cell under RA and T induction stimulate the efficient generation of MGLCs in vitro through activating TGFβ-SMAD2/3, JAK2-STAT3, and AKT pathways. Among them, JAK2-STAT3 and AKT pathways are being first reported to show involvement of in vitro generation of MGLCs during ADMSC co-culturing with SCs

Forest plot of primary lesion patency rates at 6 months.

Forest plot of primary lesion patency rates at 6 months.</p