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Lingjun Wen, Can Luo, Xinyi Chen, Tianyao Liu, Xianping Li,* Min Wang* Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, People’s Republic of China*These authors contributed equally to this workCorrespondence: Min Wang; Xianping Li, Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, 139 Renmin Middle Road, Changsha, 410011, People’s Republic of China, Tel +86 13298697558, Email wangmin0000@csu.edu.cn; xianpingli2017@csu.edu.cnPurpose: We aimed to evaluate the in vitro antibacterial effects of combination of cefepime/avibactam against carbapenem-resistant Klebsiella pneumonia (CRKP) and explore the resistance mechanism of FEP/AVI.Patients and Methods: This study explored the in vitro antibacterial activities of ceftazidime/avibactam (CAZ/AVI) and cefepime/avibactam (FEP/AVI) against 40 and 76 CRKP clinical isolates. Proteomics and metabolomics were employed to investigate the resistance mechanisms of CRKP to FEP/AVI.Results: FEP/AVI (MIC50/MIC90 0.5/4-64/4 μg/mL, resistance rate 17.1%) showed better antibacterial activity against CRKP than CAZ/AVI (MIC50/MIC90 4/4-128/4 μg/mL, resistance rate 20%) in vitro. Bioinformatics analysis showed that the differentially expressed proteins (DEPs) were enriched in alanine, aspartate and glutamate metabolism, and ribosome. Remarkably, transcriptional and translational activity-related pathways were inhibited in FEP/AVI resistant CRKP. Overlap analysis suggested that H-NS might play an important role in resistance to FEP/AVI in CRKP. The mRNA levels of DEPs-related genes (adhE, gltB, purA, ftsI and hns) showed the same trends as DEPs in FEP/AVI susceptible and resistant strains. FEP/AVI resistant isolates demonstrated stronger biofilm formation capacity than susceptible isolates. Metabolomics results showed that disturbed metabolites were mainly lipids, and adenine was decreased in FEP/AVI resistant CRKP.Conc

Drought events are increasingly affecting the planet's biodiversity. While shrinking body size in response to drought has been observed in many vertebrate animals, whether this rule applies to microscopic animals and the mechanisms during this process remains largely unknown. To address this knowledge gap, we conducted a regional-scale investigation and a microcosm experiment to systematically evaluate the impact of drought stress on the body size of the most abundant soil animals on Earth – nematodes – across various biological scales, including community, population and individual levels. Our results showed that nematode body size declined with drought stress at all biological scales, including a community shift toward smaller-sized species, a smaller body size at the population scale, and a decrease in size-at-age of individuals. Additionally, we designed a petri dish experiment to examine the reversible plasticity of body size under drought stress using a drought-tolerant nematode species. We found that while nematode body size could not be fully reversed when drought stress was alleviated in the offspring generation, offspring from parents that experienced severe drought conditions could acquire tolerance, leading to a relatively smaller reduction in overall body size compared to those from parents that suffered no or light drought conditions. Overall, our study suggests that the increasing frequency of drought events at the global scale will lead to a reduction in soil nematode body size, potentially causing far-reaching consequences for additional changes in the climate, as well as nutrient cycling in soils.

Anthropogenic land use is threatening global biodiversity. As one of the most abundant animals on Earth, nematodes occupy several key positions in belowground food webs and contribute to many ecosystem functions and services. However, the effects of land use on nematode abundance and its determinants remain poorly understood at a global scale. To characterize nematodes' responses to land use across trophic groups, we used a dataset of 6,825 soil samples globally to assess how nematode abundance varies among regional land-use types (i.e. primary vegetation, secondary vegetation, pasture, cropland and urban) and local land-use intensities (i.e. human-managed or not). We also quantified the interactive effects of land use and environmental predictors (i.e. mean annual temperature, annual precipitation, soil organic carbon, soil pH, global vegetation biomass and global vegetation productivity) on nematode abundance. We found that total nematode abundance and the abundance of bacterivores, fungivores, herbivores, omnivores and predators generally increased or were not affected under management across land-use types. Specifically, the most numerically abundant bacterivores were higher in managed than in unmanaged secondary vegetation habitats and urban areas, and herbivores were more abundant in managed than in unmanaged primary and secondary vegetation habitats. Furthermore, the numbers of significant environmental predictors of nematode abundance were reduced and the magnitude and the direction of the predictors were changed under management. We also found that nematode abundance was more variable and less determined by environmental factors in urban than in other land-use types. These findings challenge the view that human land use decreases animal abundance across trophic groups, but highlight that land use is altering the trophic composition of soil nematodes and its relationships with the environment at the global scale.

Time-dependent convection-diffusion problems is considered, particularly when the diffusivity is very small and sharp layers exist in the solutions. Nonphysical oscillations may occur in the numerical solutions when using regular mesh with standard computational methods. In this work, we develop a moving mesh SUPG (MM-SUPG) method, which integrates the streamline upwind Petrov-Galerkin (SUPG) method with the moving mesh partial differential equation (MMPDE) approach. The proposed method is designed to handle both isotropic and anisotropic diffusivity tensors. For the isotropic case, we focus on improving the stability of the numerical solution by utilizing both artificial diffusion from SUPG and mesh adaptation from MMPDE. And for the anisotropic case, we focus on the positivity of the numerical solution. We introduce a weighted diffusion tensor and develop a new metric tensor to control the mesh movement. We also develop conditions for time step size so that the numerical solution satisfies the discrete maximum principle (DMP). Numerical results demonstrate that the proposed MM-SUPG method provides results better than SUPG with fixed mesh or moving mesh without SUPG., Comment: There are 31 pages, 14 figures, and 6 tables

Anthropogenic conversion of natural to agricultural land reduces aboveground biodiversity. Yet, the overall consequences of land-use changes on belowground biodiversity at large scales remain insufficiently explored. Furthermore, the effects of conversion on different organism groups are usually determined at the taxonomic level, while an integrated investigation that includes functional and phylogenetic levels is rare and absent for belowground organisms. Here, we studied the Earth's most abundant metazoa?nematodes?to examine the effects of conversion from natural to agricultural habitats on soil biodiversity across a large spatial scale. To this aim, we investigated the diversity and composition of nematode communities at the taxonomic, functional, and phylogenetic level in 16 assemblage pairs (32 sites in total with 16 in each habitat type) in mainland China. While the overall alpha and beta diversity did not differ between natural and agricultural systems, all three alpha diversity facets decreased with latitude in natural habitats. Both alpha and beta diversity levels were driven by climatic differences in natural habitats, while none of the diversity levels changed in agricultural systems. This indicates that land conversion affects soil biodiversity in a geographically dependent manner and that agriculture could erase climatic constraints on soil biodiversity at such a scale. Additionally, the functional composition of nematode communities was more dissimilar in agricultural than in natural habitats, while the phylogenetic composition was more similar, indicating that changes among different biodiversity facets are asynchronous. Our study deepens the understanding of land-use effects on soil nematode diversity across large spatial scales. Moreover, the detected asynchrony of taxonomic, functional, and phylogenetic diversity highlights the necessity to monitor multiple facets of soil biodiversity in ecological studies such as those investigating envir

Anthropogenic conversion of natural to agricultural land reduces aboveground biodiversity. Yet, the overall consequences of land-use changes on belowground biodiversity at large scales remain insufficiently explored. Furthermore, the effects of conversion on different organism groups are usually determined at the taxonomic level, while an integrated investigation that includes functional and phylogenetic levels is rare and absent for belowground organisms. Here, we studied the Earth's most abundant metazoa—nematodes—to examine the effects of conversion from natural to agricultural habitats on soil biodiversity across a large spatial scale. To this aim, we investigated the diversity and composition of nematode communities at the taxonomic, functional, and phylogenetic level in 16 assemblage pairs (32 sites in total with 16 in each habitat type) in mainland China. While the overall alpha and beta diversity did not differ between natural and agricultural systems, all three alpha diversity facets decreased with latitude in natural habitats. Both alpha and beta diversity levels were driven by climatic differences in natural habitats, while none of the diversity levels changed in agricultural systems. This indicates that land conversion affects soil biodiversity in a geographically dependent manner and that agriculture could erase climatic constraints on soil biodiversity at such a scale. Additionally, the functional composition of nematode communities was more dissimilar in agricultural than in natural habitats, while the phylogenetic composition was more similar, indicating that changes among different biodiversity facets are asynchronous. Our study deepens the understanding of land-use effects on soil nematode diversity across large spatial scales. Moreover, the detected asynchrony of taxonomic, functional, and phylogenetic diversity highlights the necessity to monitor multiple facets of soil biodiversity in ecological studies such as those investigating environmental

As the resolution of digital images increase significantly, the processing of images becomes more challenging in terms of accuracy and efficiency. In this paper, we consider image segmentation by solving a partial differentiation equation (PDE) model based on the Mumford-Shah functional. We develop a new algorithm by combining anisotropic mesh adaptation for image representation and finite element method for solving the PDE model. Comparing to traditional algorithms solved by finite difference method, our algorithm provides faster and better results without the need to resizing the images to lower quality. We also extend the algorithm to segment images with multiple regions., Comment: 17 pages, 9 figures

Compressed sensing (CS) has become a popular field in the last two decades to represent and reconstruct a sparse signal with much fewer samples than the signal itself. Although regular images are not sparse on their own, many can be sparsely represented in wavelet transform domain. Therefore, CS has also been widely applied to represent digital images. However, an alternative approach, adaptive sampling such as mesh-based image representation (MbIR), has not attracted as much attention. MbIR works directly on image pixels and represents the image with fewer points using a triangular mesh. In this paper, we perform a preliminary comparison between the CS and a recently developed MbIR method, AMA representation. The results demonstrate that, at the same sample density, AMA representation can provide better reconstruction quality than CS based on the tested algorithms. Further investigation with recent algorithms is needed to perform a thorough comparison., Comment: 9 pages, 4 figures, 2 tables

Wang B, Wang M, Li X, Yang M, Liu L. Pharmgenomics Pers Med. 2020;13:157—165. Page 157, Abstract, Results section, the text “The mutant alleles of rs3864004 (A) and rs2293303 (T) located in CTNNB1 showed 1.513 (1.038–2.207), and 1.654 (1.020–2.683) fold increased risk of cervical cancer, respectively” should read “The mutant alleles of rs3864004 (A) and rs2293303 (T) located in CTNNB1 showed 0.661 (0.453-0.964), and 0.605 (0.373-0.981) fold risk of cervical cancer, respectively”. Page 160, Results, Association Analysis of Eight Polymorphisms with Cervical Cancer section, the text “Compared with the healthy control group, the rs3864004 A allele (OR=1.513, 95% CI=1.038–2.207, P=0.031) of the CTNNB1 gene showed significant differences in the cervical cancer group. The minor allele (T) for rs2293303 was positively associated with a higher risk for cervical cancer development (OR=1.654, 95% CI=1.020–2.683, P=0.040, Table 3)” should read “Compared with the healthy control group, the rs3864004 A allele (OR=0.661, 95% CI=0.453- 0.964, P=0.031) of the CTNNB1 gene showed significant differences in the cervical cancer group. The minor allele (T) for rs2293303 was positively associated with a lower risk for cervical cancer development (OR=0.605, 95% CI=0.373-0.981, P=0.040, Table 3)”. Table 3 on page 161, the OR (95% CI) values are incorrect. The correct Table 3 is shown below. Page 162, Discussion, second paragraph, “In the single- locus analysis, we identified that mutant alleles of rs3864004 (A) and rs2293303 (T) might be risk factors for cervical cancer” should read “In the single-locus analysis, we identified tha

Bingqi Wang, Min Wang, Xianping Li, Min Yang, Lei Liu Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, People’s Republic of ChinaCorrespondence: Min WangDepartment of Laboratory Medicine, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha 410011, Hunan, People’s Republic of ChinaTel/Fax +86 132 9869 7558Email wangmin0000@csu.edu.cnBackground: Cervical cancer is the fourth most common and fatal tumor among women worldwide. The Wnt/β-catenin signaling pathway was etiologically involved in the cervical cancer model. Herein, we aimed to investigate whether germline genetic variations within the Wnt/β-catenin pathway can be genetic risk factors of cervical cancer.Patients and Methods: A total of 305 samples (147 patients, 158 controls) were included. Eight genetic variations located in APC (rs454886), GSK3β (rs3755557), CTNNB1 (rs11564475, rs1798802, rs3864004, rs2293303, and rs4135385), and TCF7L2 (rs7903146) were genotyped via Sanger sequencing. The χ 2 test and non-conditional logistic regression were used in the single-locus analysis. Gene–gene interactions and haplotype construction in case–control samples were performed by the GMDR method and Haploview software, respectively.Results: The frequency of CTNNB1 rs1798802 GA+AA genotype was significantly lower in cervical cancer patients adjusted for age (OR=0.626, 95% CI=0.398– 0.984). The mutant alleles of rs3864004 (A) and rs2293303 (T) located in CTNNB1 showed 1.513 (1.038– 2.207), and 1.654 (1.020– 2.683) fold increased risk of cervical cancer, respectively. Haplotype analysis showed no association between haplotypes of the CTNNB1 gene and cervical cancer risk. No significant contribution of interactions among genes in the Wnt pathway was identified.Conclusion: We concluded that the genetic variants in the CTNNB

Earthworms have been perceived as benevolent soil engineers since the time of Charles Darwin, but several recent syntheses link earthworm activities to higher greenhouse gas emissions, less soil biodiversity, and inferior plant defense against pests. Our study provides new field-based evidence of the multiple direct and indirect impacts of earthworms on ecosystem functions within an ecological multifunctionality framework (i.e., aggregated measures of the ability of ecosystems to simultaneously provide multiple ecosystem functions). Data from a 13-year field experiment describing 21 ecosystem functions showed that earthworm presence generally enhanced multifunctionality by indirect rather than direct effects. Specifically, earthworms enhanced multifunctionality by shifting the functional composition toward a soil community favoring the bacterial energy channel and strengthening the biotic associations of soil microbial and microfaunal communities. However, earthworm-mediated changes in soil physical structure, pH, and taxonomic diversity were not related to multifunctionality. We conclude that the coordinated actions of earthworms and their associated soil biota were responsible for the maintenance of multifunctionality at high levels in this rice-wheat cropping system. Management of crop residue inputs and reduction of soil physicochemical disturbances should encourage beneficial earthworm effects and support multiple ecosystem services that are vital to sustainable agriculture.

Earthworms have been perceived as benevolent soil engineers since the time of Charles Darwin, but several recent syntheses link earthworm activities to higher greenhouse gas emissions, less soil biodiversity, and inferior plant defense against pests. Our study provides new field-based evidence of the multiple direct and indirect impacts of earthworms on ecosystem functions within an ecological multifunctionality framework (i.e., aggregated measures of the ability of ecosystems to simultaneously provide multiple ecosystem functions). Data from a 13-year field experiment describing 21 ecosystem functions showed that earthworm presence generally enhanced multifunctionality by indirect rather than direct effects. Specifically, earthworms enhanced multifunctionality by shifting the functional composition toward a soil community favoring the bacterial energy channel and strengthening the biotic associations of soil microbial and microfaunal communities. However, earthworm-mediated changes in soil physical structure, pH, and taxonomic diversity were not related to multifunctionality. We conclude that the coordinated actions of earthworms and their associated soil biota were responsible for the maintenance of multifunctionality at high levels in this rice-wheat cropping system. Management of crop residue inputs and reduction of soil physicochemical disturbances should encourage beneficial earthworm effects and support multiple ecosystem services that are vital to sustainable agriculture.

Triangular meshes have gained much interest in image representation and have been widely used in image processing. This paper introduces a framework of anisotropic mesh adaptation (AMA) methods to image representation and proposes a GPRAMA method that is based on AMA and greedy-point removal (GPR) scheme. Different than many other methods that triangulate sample points to form the mesh, the AMA methods start directly with a triangular mesh and then adapt the mesh based on a user-defined metric tensor to represent the image. The AMA methods have clear mathematical framework and provides flexibility for both image representation and image reconstruction. A mesh patching technique is developed for the implementation of the GPRAMA method, which leads to an improved version of the popular GPRFS-ED method. The GPRAMA method can achieve better quality than the GPRFS-ED method but with lower computational cost., Comment: 25 pages, 15 figures