Coexisting Vortices and Antivortices Generated by Dually Gauged Harmonic Maps

In this paper we first formulate a dually gauged harmonic map model, suggested from a product Abelian Higgs field theory arising in impurity-inspired field theories, and obtain a new BPS system of equations governing coexisting vortices and antivortices, which are topologically characterized by the first Chern class of the underlying Hermitian bundle and the Thom class of the associated dual bundle. We then establish existence and uniqueness theorems for such vortices. For the equations over a compact surface, we obtain necessary and sufficient conditions for the existence of solutions. For the equations over the full plane, we obtain all finite-energy solutions. Besides, we also present precise expressions giving the values of various physical quantities of the solutions, including magnetic charges and energies, in terms of the total numbers of vortices and antivortices, of two species, and the coupling parameters involved.Comment: 30 pages, 1 figur

Automatic Gradient Descent: Deep Learning without Hyperparameters

The architecture of a deep neural network is defined explicitly in terms of the number of layers, the width of each layer and the general network topology. Existing optimisation frameworks neglect this information in favour of implicit architectural information (e.g. second-order methods) or architecture-agnostic distance functions (e.g. mirror descent). Meanwhile, the most popular optimiser in practice, Adam, is based on heuristics. This paper builds a new framework for deriving optimisation algorithms that explicitly leverage neural architecture. The theory extends mirror descent to non-convex composite objective functions: the idea is to transform a Bregman divergence to account for the non-linear structure of neural architecture. Working through the details for deep fully-connected networks yields automatic gradient descent: a first-order optimiser without any hyperparameters. Automatic gradient descent trains both fully-connected and convolutional networks out-of-the-box and at ImageNet scale. A PyTorch implementation is available at https://github.com/jxbz/agd and also in Appendix B. Overall, the paper supplies a rigorous theoretical foundation for a next-generation of architecture-dependent optimisers that work automatically and without hyperparameters

Decreased heritability and emergence of novel genetic effects on pulse wave velocity from youth to young adulthood

Increased arterial stiffness measured by pulse wave velocity (PWV) is an important parameter in the assessment of cardiovascular risk. Our previous longitudinal study has demonstrated that carotid-distal PWV showed reasonable stability throughout youth and young adulthood. This stability might be driven by genetic factors that are expressed consistently over time. We aimed to illustrate the relative contributions of genetic and environmental factors to the stability of carotid-distal PWV from youth to young adulthood. We also examined potential ethnic differences. For this purpose, carotid-distal PWV was measured twice in 497 European American (EA) and African American (AA) twins, with an average interval time of 3 years. Twin modelling on PWV showed that heritability decreased over time (62-35%), with the nonshared environmental influences becoming larger. There was no correlation between the nonshared environmental factors on PWV measured at visit 1 and visit 2, with the phenotypic tracking correlation (r=0.32) completely explained by shared genetic factors over time. Novel genetic influences were identified accounting for a significant part of the variance (19%) at the second measurement occasion. There was no evidence for ethnic differences. In summary, novel genetic effects appear during development into young adulthood and account for a considerable part of the variation in PWV. Environmental influences become larger with age for PWV

Habitat adaptation drives speciation of a Streptomyces species with distinct habitats and disparate geographic origins

Microbial diversification is driven by geographic and ecological factors, but how the relative importance of these factors varies among species, geographic scales, and habitats remains unclear. Streptomyces, a genus of antibiotic-producing, spore-forming, and widespread bacteria, offers a robust model for identifying the processes underlying population differentiation. We examined the population structure of 37 Streptomyces olivaceus strains isolated from various sources, showing that they diverged into two habitat-associated (free-living and insect-associated) and geographically disparate lineages. More frequent gene flow within than between the lineages confirmed genetic isolation in S. olivaceus. Geographic isolation could not explain the genetic isolation; instead, habitat type was a strong predictor of genetic distance when controlling for geographic distance. The identification of habitat-specific genetic variations, including genes involved in regulation, resource use, and secondary metabolism, suggested a significant role of habitat adaptation in the diversification process. Physiological assays revealed fitness trade-offs under different environmental conditions in the two lineages. Notably, insect-associated isolates could outcompete free-living isolates in a free-iron-deficient environment. Furthermore, substrate (e.g., sialic acid and glycogen) utilization but not thermal traits differentiated the two lineages. Overall, our results argue that adaptive processes drove ecological divergence among closely related streptomycetes, eventually leading to dispersal limitation and gene flow barriers between the lineages. S. olivaceus may best be considered a species complex consisting of two cryptic species.China Ocean Mineral Resources R&D Association/[DY135-B2-02]/CONRA/ChinaNational Natural Science Foundation of China/[32070001 and 91751118]/NSFC/ChinaRV KEXUE/[KEXUE2019GZ05]//ChinaChinese Academy of Sciences/[KEXUE2019GZ05]/CAS/ChinaUniversidad de Costa Rica/[801-B0-530]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Estructuras Microscópicas (CIEMIC)UCR::Vicerrectoría de Docencia::Ingeniería::Facultad de Ingeniería::Escuela de Ciencias de la Computación e Informátic

Evaluating the Efficiency of Treatment Comparison in Crossover Design by Allocating Subjects Based On Ranked Auxiliary Variable

The validity of statistical inference depends on proper randomization methods. However, even with proper randomization, we can have imbalanced with respect to important characteristics. In this paper, we introduce a method based on ranked auxiliary variables for treatment allocation in crossover designs using Latin squares models. We evaluate the improvement of the efficiency in treatment comparisons using the proposed method. Our simulation study reveals that our proposed method provides a more powerful test compared to simple randomization with the same sample size. The proposed method is illustrated by conducting an experiment to compare two different concentrations of titanium dioxide nanofiber (TDNF) on rats for the purpose of comparing weight gain

Proteomic analysis of young leaves at three developmental stages in an albino tea cultivar

Abstract Background White leaf No.1 is a typical albino tea cultivar grown in China and it has received increased attention in recent years due to the fact that white leaves containing a high level of amino acids, which are very important components affecting the quality of tea drink. According to the color of its leaves, the development of this tea cultivar is divided into three stages: the pre-albinistic stage, the albinistic stage and the regreening stage. To understand the intricate mechanism of periodic albinism, a comparative proteomic approach based on two-dimensional electrophoresis (2-DE) and mass spectrometry was adopted first time to identify proteins that changed in abundance during the three developmental periods. Results The 2-DE results showed that the expression level of 61 protein spots varied markedly during the three developmental stages. To analyze the functions of the significantly differentially expressed protein spots, 30 spots were excised from gels and analyzed by matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry. Of these, 26 spots were successfully identified. All identified protein spots were involved in metabolism of carbon, nitrogen and sulfur, photosynthesis, protein processing, stress defense and RNA processing, indicating these physiological processes may play crucial roles in the periodic albinism. Quantitative real-time RT-PCR analysis was used to assess the transcriptional level of differentially expressed proteins. In addition, the ultrastructural studies revealed that the etioplast-chloroplast transition in the leaf cell of White leaf No. 1 was inhibited and the grana in the chloroplast was destroyed at the albinistic stage. Conclusions In this work, the proteomic analysis revealed that some proteins may have important roles in the molecular events involved in periodic albinism of White leaf No. 1 and identificated many attractive candidates for further investigation. In addition, the ultrastructural studies revealed that the change in leaf color of White leaf No. 1 might be a consequence of suppression of the etioplast-chloroplast transition and damage to grana in the chloroplast induced by temperature. These results provide much useful information to improve our understanding of the mechanism of albinism in the albino tea cultivar.</p

Genetic and Environmental Effects on Gene Expression Signatures of Blood Pressure A Transcriptome-Wide Twin Study

Recently, 2 transcriptome-wide studies identified 40 genes that were differentially expressed in relation to blood pressure. However, to what extent these BP-related gene expression signatures and their associations with BP are driven by genetic or environmental factors has not been investigated. In this study of 391 twins (193 twin pairs and 5 singletons; age 55-69 years; 40% male; 57% monozygous) recruited from the Finnish Twin Cohort, transcriptome-wide data on peripheral leukocytes were obtained using the Illumina HT12 V4 array. Our transcriptome-wide analysis identified 1 gene (MOK [MAPK/MAK/MRK overlapping kinase], P=7.16x10(-8)) with its expression levels associated with systolic BP at the cutoff of false-discovery rate</p

Genome-wide identification of the expansin gene family in netted melon and their transcriptional responses to fruit peel cracking

IntroductionFruit cracking not only affects the appearance of netted melons (Cucumis melo L. var. reticulatus Naud.) but also decreases their marketability.MethodsHerein, to comprehensively understand the role of expansin (EXP) proteins in netted melon, bioinformatics methods were employed to discover the EXP gene family in the melon genome and analyze its characteristic features. Furthermore, transcriptomics analysis was performed to determine the expression patterns of melon EXP (CmEXP) genes in crack-tolerant and crack-susceptible netted melon varieties.DiscussionThirty-three CmEXP genes were identified. Chromosomal location analysis revealed that CmEXP gene distribution was uneven on 12 chromosomes. In addition, phylogenetic tree analysis revealed that CmEXP genes could be categorized into four subgroups, among which the EXPA subgroup had the most members. The same subgroup members shared similar protein motifs and gene structures. Thirteen duplicate events were identified in the 33 CmEXP genes. Collinearity analysis revealed that the CmEXP genes had 50, 50, and 44 orthologous genes with EXP genes in cucumber, watermelon, and Arabidopsis, respectively. However, only nine orthologous EXP genes were observed in rice. Promoter cis-acting element analysis demonstrated that numerous cis-acting elements in the upstream promoter region of CmEXP genes participate in plant growth, development, and environmental stress responses. Transcriptomics analysis revealed 14 differentially expressed genes (DEGs) in the non-cracked fruit peels between the crack-tolerant variety ‘Xizhoumi 17’ (N17) and the crack-susceptible variety ‘Xizhoumi 25’ (N25). Among the 14 genes, 11 were upregulated, whereas the remaining three were downregulated in N17. In the non-cracked (N25) and cracked (C25) fruit peels of ‘Xizhoumi 25’, 24 DEGs were identified, and 4 of them were upregulated, whereas the remaining 20 were downregulated in N25. In the two datasets, only CmEXPB1 exhibited consistently upregulated expression, indicating its importance in the fruit peel crack resistance of netted melon. Transcription factor prediction revealed 56 potential transcription factors that regulate CmEXPB1 expression.ResultsOur study findings enrich the understanding of the CmEXP gene family and present candidate genes for the molecular breeding of fruit peel crack resistance of netted melon

Treatment of Rheumatoid Arthritis Using Combination of Methotrexate and Tripterygium Glycosides Tablets—A Quantitative Plasma Pharmacochemical and Pseudotargeted Metabolomic Approach

Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by chronic destructive synovitis and is associated with progressive disability, systemic difficulties, premature death, and socioeconomic costs. Early intervention with disease-modifying antirheumatic drugs (DMARDs) like methotrexate (MTX) and its combination regimen would provide obvious benefits to patients, healthcare systems and society. MTX and tripterygium glycosides tablets (TGTS) are most frequently prescribed medicines for RA, and the combination of them occurs frequently in anti-RA prescriptions. While the underlying combination mechanisms and the affected variation of drug blood level remain unclear. According to the American College of Rheumatology criteria for improvement, clinical evaluation following three treatment groups (i.e., MTX and TGTS mono- and combined groups) were carried out at baseline and at the end of 12 weeks in a randomized controlled clinical trial. To monitor the affected variation of drug blood level and perturbation of metabolites caused by MTX plus TGTS combined to treat active RA, the collected plasma samples were analyzed using RRLC-QqQ-MS and UHPLC-QE Orbitrap HRMS instruments. As a result, 39 metabolites including 7 MTX-related metabolites, 13 TGTS-related migratory ingredients and 19 characteristic endogenous metabolites, were quantitatively determined in plasma samples of RA patients after oral administration. The potential mechanism of MTX and TGTS combination were preliminarily elucidated on the aspect of clinical biochemical test indicators integrated with quantitative plasma pharmacochemistry and the pseudotargeted metabolomics