An efficient algorithm for the ℓp\ell_{p} norm based metric nearness problem

Given a dissimilarity matrix, the metric nearness problem is to find the nearest matrix of distances that satisfy the triangle inequalities. This problem has wide applications, such as sensor networks, image processing, and so on. But it is of great challenge even to obtain a moderately accurate solution due to the $O(n^{3})$ metric constraints and the nonsmooth objective function which is usually a weighted $\ell_{p}$ norm based distance. In this paper, we propose a delayed constraint generation method with each subproblem solved by the semismooth Newton based proximal augmented Lagrangian method (PALM) for the metric nearness problem. Due to the high memory requirement for the storage of the matrix related to the metric constraints, we take advantage of the special structure of the matrix and do not need to store the corresponding constraint matrix. A pleasing aspect of our algorithm is that we can solve these problems involving up to $10^{8}$ variables and $10^{13}$ constraints. Numerical experiments demonstrate the efficiency of our algorithm. In theory, firstly, under a mild condition, we establish a primal-dual error bound condition which is very essential for the analysis of local convergence rate of PALM. Secondly, we prove the equivalence between the dual nondegeneracy condition and nonsingularity of the generalized Jacobian for the inner subproblem of PALM. Thirdly, when $q(\cdot)=\|\cdot\|_{1}$ or $\|\cdot\|_{\infty}$, without the strict complementarity condition, we also prove the equivalence between the the dual nondegeneracy condition and the uniqueness of the primal solution

The contribution of Alu exons to the human proteome.

BackgroundAlu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of Alu exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements, such as Alu elements, are restricted to regulatory functions and have not had adequate evolutionary time to be incorporated into stable, functional proteins.ResultsWe adopt a proteotranscriptomics approach to systematically assess the contribution of Alu exons to the human proteome. Using RNA sequencing, ribosome profiling, and proteomics data from human tissues and cell lines, we provide evidence for the translational activities of Alu exons and the presence of Alu exon derived peptides in human proteins. These Alu exon peptides represent species-specific protein differences between primates and other mammals, and in certain instances between humans and closely related primates. In the case of the RNA editing enzyme ADARB1, which contains an Alu exon peptide in its catalytic domain, RNA sequencing analyses of A-to-I editing demonstrate that both the Alu exon skipping and inclusion isoforms encode active enzymes. The Alu exon derived peptide may fine tune the overall editing activity and, in limited cases, the site selectivity of ADARB1 protein products.ConclusionsOur data indicate that Alu elements have contributed to the acquisition of novel protein sequences during primate and human evolution

Construction of stable Ta3N5/g-C3N4 metal/non-metal nitride hybrids with enhanced visible-light photocatalysis

In this paper, a novel Ta3N5/g-C3N4 metal/non-metal nitride hybrid was successfully synthesized by a facile impregnation method. The photocatalytic activity of Ta3N5/g-C3N4 hybrid nitrides was evaluated by the degradation of organic dye rhodamine B (RhB) under visible light irradiation, and the result indicated that all Ta3N5/g-C3N4 samples exhibited distinctly enhanced photocatalytic activities for the degradation of RhB than pure g-C3N4. The optimal Ta3N5/g-C3N4 composite sample, with Ta3N5 mass ratio of 2%, demonstrated the highest photocatalytic activity, and its degradation rate constant was 2.71 times as high as that of pure g-C3N4. The enhanced photocatalytic activity of this Ta3N5/g-C3N4 metal/metal-free nitride was predominantly attributed to the synergistic effect which increased visible-light absorption and facilitated the efficient separation of photoinduced electrons and holes. The Ta3N5/g-C3N4 hybrid nitride exhibited excellent photostability and reusability. The possible mechanism for improved photocatalytic performance was proposed. Overall, this work may provide a facile way to synthesize the highly efficient metal/metal-free hybrid nitride photocatalysts with promising applications in environmental purification and energy conversion

Changes in global climate heterogeneity under the 21st century global warming

Publisher Copyright: © 2021 The Author(s)Variations in climate types are commonly used to describe changes in natural vegetation cover in response to global climate change. However, few attempts have been made to quantify the heterogeneous dynamics of climate types. In this study, based on the Coupled Model Intercomparison Project phase 5 (CMIP5) historical and representative concentration pathway (RCP) runs from 18 global climate models, we used Shannon's Diversity Index (SHDI) and Simpson's Diversity Index (SIDI) to characterise of global climate heterogeneity from a morphological perspective. Our results show that global climate heterogeneity calculated by the SHDI/SIDI indices decreased from 1901 to 2095 at a significance level of 0.01. As radiative forcing intensified from RCP 2.6 to 8.5, the SHDI/SIDI decreased significantly. Furthermore, we observed that the spatial distribution of global climate heterogeneity was significantly reduced, with a pronounced latitudinal trend. Sensitivity analysis indicated that the temperature increase played a more significant role in reducing global climate heterogeneity than precipitation under the three warming scenarios, which is possibly attributed to anthropogenic forcing. Our findings suggest that the dynamics of global climate heterogeneity can be an effective means of quantifying global biodiversity loss.Peer reviewe

Genome Wide Association Studies for Milk Production Traits in Chinese Holstein Population

Genome-wide association studies (GWAS) based on high throughput SNP genotyping technologies open a broad avenue for exploring genes associated with milk production traits in dairy cattle. Motivated by pinpointing novel quantitative trait nucleotide (QTN) across Bos Taurus genome, the present study is to perform GWAS to identify genes affecting milk production traits using current state-of-the-art SNP genotyping technology, i.e., the Illumina BovineSNP50 BeadChip. In the analyses, the five most commonly evaluated milk production traits are involved, including milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP) and milk protein percentage (PP). Estimated breeding values (EBVs) of 2,093 daughters from 14 paternal half-sib families are considered as phenotypes within the framework of a daughter design. Association tests between each trait and the 54K SNPs are achieved via two different analysis approaches, a paternal transmission disequilibrium test (TDT)-based approach (L1-TDT) and a mixed model based regression analysis (MMRA). In total, 105 SNPs were detected to be significantly associated genome-wise with one or multiple milk production traits. Of the 105 SNPs, 38 were commonly detected by both methods, while four and 63 were solely detected by L1-TDT and MMRA, respectively. The majority (86 out of 105) of the significant SNPs is located within the reported QTL regions and some are within or close to the reported candidate genes. In particular, two SNPs, ARS-BFGL-NGS-4939 and BFGL-NGS-118998, are located close to the DGAT1 gene (160bp apart) and within the GHR gene, respectively. Our findings herein not only provide confirmatory evidences for previously findings, but also explore a suite of novel SNPs associated with milk production traits, and thus form a solid basis for eventually unraveling the causal mutations for milk production traits in dairy cattle

Patterns of deep fine root and water utilization amongst trees, shrubs and herbs in subtropical pine plantations with seasonal droughts

IntroductionSeasonal droughts will become more severe and frequent under the context of global climate change, this would result in significant variations in the root distribution and water utilization patterns of plants. However, research on the determining factors of deep fine root and water utilization is limited.MethodsWe measured the fine root biomass and water utilization of trees, shrubs and herbs, and soil properties, light transmission, and community structure parameters in subtropical pine plantations with seasonal droughts.Results and DiscussionWe found that the proportion of deep fine roots (below 1 m depth) is only 0.2-5.1%, but that of deep soil water utilization can reach 20.9-38.6% during the dry season. Trees improve deep soil water capture capacity by enhancing their dominance in occupying deep soil volume, and enhance their deep resource foraging by increasing their branching capacity of absorptive roots. Shrubs and herbs showed different strategies for deep water competition: shrubs tend to exhibit a “conservative” strategy and tend to increase individual competitiveness, while herbs exhibited an “opportunistic” strategy and tend to increase variety and quantity to adapt to competitions.ConclusionOur results improve our understanding of different deep fine root distribution and water use strategies between overstory trees and understory vegetations, and emphasize the importance of deep fine root in drought resistance as well as the roles of deep soil water utilization in shaping community assembly

Development of reduced-salt gel of silver carp meat batter using low frequency ultrasound: Effect on color, texture, cooking loss and microstructure

Purpose: To develop reduced-salt silver carp meat gels using low frequency ultrasound. Methods: Silver carp meat batters were prepared with 0.5, 1 (reduced-salt) and 2 % (regular salt), and sonicated (20 KHz, 500 W) for 30 and 40 min, or unsonicated (control). Changes in gel properties were evaluated in terms of color, texture, cooking loss and microstructure using color measurement, puncture test, cooking loss and scanning electron microscopic (SEM) analysis, respectively. Results: Ultrasound and salt exposure led to marked effects on color, texture and cooking loss in fish meat gels (p < 0.05). Reduction in salt content increased the lightness (L*) and cooking loss; and also decreased the sample values of greenness (-a*), breaking force, rupture distance and gel strength. Scanning electron microscopy (SEM) on regular-salt level samples showed that ultrasonic exposure decreased dense aggregates and increased the number and distribution of small cavity samples. Reduced-salt samples (1 % salt) subjected to 30 min sonication had better color (lighter) than control (0 min sonication), better texture (higher gel strength) and cooking loss comparable to that of regular-salt level sample subjected to 30 min sonication, and similar to microstructures from normal salt samples without ultrasound exposure. Conclusion: Low frequency ultrasound is suitable for preparing reduced-salt fish meat gels under suitable ultrasonic conditions

Ag nanoparticles/PPV composite nanofibers with high and sensitive opto-electronic response

The novel Ag nanoparticles/poly(p-phenylene vinylene) [PPV] composite nanofibers were prepared by electrospinning. The transmission electron microscope image shows that the average diameter of composite fibers is about 500 nm and Ag nanoparticles are uniformly dispersed in the PPV matrix with an average diameter of about 25 nm. The Fourier transform infrared spectra suggest that there could be a coordination effect to a certain extent between the Ag atom and the π system of PPV, which is significantly favorable for the dissociation of photoexcitons and the charge transfer at the interface between the Ag nanoparticle and the PPV. The Au top electrode device of the single Ag/PPV composite nanofiber exhibits high and sensitive opto-electronic responses. Under light illumination of 5.76 mW/cm2 and voltage of 20 V, the photocurrent is over three times larger than the dark current under same voltage, which indicates that this kind of composite fiber is an excellent opto-electronic nanomaterial